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Why the title "Second Season"?
So, the Monogatari series has four season, and soon will be five, and if we look at the production order, based on this question, and this Wikipedia page it will be:

Bakemonogatari (2009–2010)
Nisemonogatari (2012)
Nekomonogatari (Kuro) (2012)
Monogatari Series: Second Season (2013)
Monogatari Series: Second Season + α or Hanamonogatari (2014)

As you can see, "Second Season" is the fourth and fifth season of anime, so why the title "Second Season"?

afaik, some of the shows such as nekomonogatari aren't called seasons because of their length

then it should be "Third Season"

yeah I'm not sure about Nisemonogatari

I am quite sure "Second Season" refers to the "season"/arc of the novels, rather than anime season. The novels in the Monogatari series are divided into 3 arcs/seasons, and Nekomonogatari , Kabukimonogatari, Hanamonogatari, Onimonogatari, Otorimonogatari, Koimonogatari all belongs to the 2nd season/arc of the novel series. As to why the novels are divided as such, I am not too sure of the reasons.

@nhahtdh I think you're right, you should post that as answer

From what I observe, the season in novel is based on whose POV the story is narrated? The first season is from Araragi's view, where the second season is from the girls' view?

@田中アキ Except that Kabukimonogatari (Mayoi Jiangshi), and I believe also Onimonogatari (Shinobu Time), are narrated by Koyomi and not by the heroine. Also, Koimonogatari (Hitagi End) is narrated by Kaiki Deishu, though you could say that Kaiki is the "heroine" of Hitagi End.

Second Season refers to the light novel series, not the anime
The word Second in the anime title Monogatari Series: Second Season is not based on the number of times the series has been animated (which is the usual practice), but rather based on the fact that the anime adapts the content from the Second Season of the Monogatari Series, which consists of 6 volumes (listed in order of publication): Nekomonogatari (White), Kabukimonogatari, Hanamonogatari, Otorimonogatari, Onimonogatari, and Koimonogatari.
The anime Monogatari Series: Second Season (summer 2013) has adapted (listed in airing order) Nekomonogatari (White), Kabukimonogatari, Otorimonogatari, Onimonogatari, Koimonogatari. And this summer (2014), Hanamonogatari will be animated under the title Monogatari Series: Second Season Hanamonogatari.
Earliest usage of the term
The term Second Season has been in used since mid 2011 in Monogatari Series article on Wikipedia.
It also has been used on an anime news site in March 2011, regarding the release of Hanamonogatari (emphasis mine).

第変話「するがデビル」を収録した西尾維新『花物語』の発売日が3月29日に決まった。『花物語』は化物語シリーズ セカンドシーズン『猫物語(白)』『傾物語』に次ぐ第3弾。

How the term comes to use
As for why the 6 volumes are collectively called Second Season, according to Wikipedia article of Monogatari Series in Japanese:

『猫物語（黒）』で当初の予定であった暦とその周辺の人物の物語は一通り終了したが、『化物語』のアニメ化に触発されて「セカンドシーズン」が発表された。

My own translation1:
1 Feel free to edit in a correct translation.

Although the series was initially planned to end at Nekomonogatari (White), at which point the series have finished telling the story about Koyomi and all the people around him, Nishio Ishin was inspired by the anime adaptation of Bakemonogatari and announced the "Second Season".

The old version of the article noted the date of the announcement being June 2010.
Then, Bakemonogatari (2 volumes), Kizumonogatari, Nisemonogatari (2 volumes), Nekomonogatari (Black) are collectively called First Season for the sake of convenience after the Second Season was announced.

セカンドシーズン発表後に便宜上「ファーストシーズン」と呼ばれるようになった。

Unfortunately, the article (old or new) didn't cite any source regarding the announcement of the Second Season of the novel.
Reference

〈物語〉シリーズ - Wikipedia. Version July 21st, 2014.
〈物語〉シリーズ - Wikipedia. Version July 7th, 2011.

I'll take a shot at this. The Bakemonogatari wiki groups the Bakemonogatari volumes, the Nisemonogatari volumes, Kizumonogatari, and Nekomonogatari Black together as Season 1. The stories adapted in the Second Season anime, plus Suruga Devil, are grouped as Season 2, and the rest are Season 3. Wikipedia corroborates this. So it is based on the novels, as nhahtdh says. And of course, since the second season anime covers five different novels (Neko White, Kabukimonogatari, Otorimonogatari, Onimonogatari, and Koimonogatari), they couldn't just reuse the name of the novel like with the Bake and Nise anime series.
As to why the novels are grouped like this, it's hard to say, so I'll speculate wildly. First of all, notice that if the Monogatari series had used a regular season (26 episodes) for the anime, instead of short seasons plus ONAs, that would just about cover Bake (15 episodes) and Nise (11 episodes), and then we'd have a four-episode Neko Black OVA and possibly a Kizu movie, if it ever got made in this alternate reality. It's possible that Nisio Isin recognized this when he decided to assign those novels to the first season. Also note that the second season did fit fairly neatly into one 26-episode season, which could have contained Hanamonogatari if they'd cut out all the review episodes.
Second, look at the content of the stories. Bake and Nise together cover a single story for each heroine, including Karen and Tsukihi. The other two first-season entries, Kizu and Neko Black, are prequels, and Kizu is sort of the first Shinobu story. The second season novels all take place after the first season novels, and give a second story for each heroine, narrated by that heroine in many cases, with the exceptions of Kabuki-, Oni-, and Koimonogatari. The second season stories are also tied together by the presence of Ougi.
I have no exposure to the third season novels, so I can't say how they fit in. But it does make some sense that the novels would be grouped like this, even though the anime adaptations didn't carry this grouping over with the first season novels.


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Is the story of "Welcome to the N.H.K." about hikikomori based on a real conspiracy?
After watching Welcome to the N.H.K., it got me wondering if this story had been based on a real conspiracy.
According to Wikipedia,

[...] The story revolves around a 22-year-old asocial individual who gets aid from a strange girl who seems to know a lot about him, despite never having met him before. A common theme throughout the story deals with the hardships of life and how people must deal with them in their own way.
[...]
In Japan, NHK refers to the public broadcaster Nippon Hōsō Kyōkai, but within the series, the main character believes it stands for Nihon Hikikomori Kyōkai (日本引きこもり協会, The Japanese Hikikomori Association), which is a reference to the protagonist's claim of a subversive conspiracy led by NHK (the real-life broadcaster) to create hikikomori. [...]

I haven't read through the article about hikikomori's yet, but as far as I remember, too many people end up living in seclusion in Japan for it to be just a coincidence.
Was there ever a conspiracy or claims that there might be a company or organisation that would promote people to live their lives in seclusion?

"Being alone is best. I mean, it's true, isn't it? In the end you'll be absolutely alone; therefore, being alone is natural. If you accept that, nothing bad can happen..."

I'm pretty sure Welcome to the N.H.K. isn't based on an actual conspiracy story. It's not mentioned in any interviews or commentary sections of the media.
I would imagine however, that the conspiracy is somewhat based on the author Tatsuhiko Takimoto's personal experience living as a self-proclaimed "top-runner" hikkomori. In the light novel afterword, it informs us that he primarily lives off royalties of his novels.
The 'conspiracy' is mostly a commentary on how the mundane life of TV and seclusion is easy to fall into - because of the attraction of broadcast media's element of fantasy, such as produced by NHK TV - and the lack of immediate consequence if should one fall into a hikkomori lifestyle. So it could seem like there are conspirators trying to keep hikkomoris as hikkomoris.
Hikkomoris feel trapped because they usually have little social or commercially valuable skills meaning it is hard to get a job or contribute to society (Especially as Japan job system is pretty much school -> college -> job or via social contacts) - and on the flip side, it is much easier to stay indoors and watch another episode of the latest airing anime.
This isn't his first novel dealing with the issue of life indirection either - Happy Negative Chainsaw Edge. So it is an issue that is close to his heart - perhaps he himself believes there is a conspiracy.
This fan blog post is a pretty great for reference for N.H.K. stuff in general

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What skills introduced prior to the formal introduction of Haki are Busoshoku Haki based?
There are 6 techniques that are the keys to Rokushiki.  Despite a claim in another answer from a well informed user that none of the CP9 members are haki users, several of these techniques seem to be rudimentary forms of Busoshoku Haki.  It seems completely reasonable that the marines would be training them in the use of Haki based skills.
In particular: Tekkai, Rokuogan, and Shigan seem to clearly be Haki based.  There are, however, some points against this including Luffy's reaction to Shigan.
Geppo and Rankyaku could feasibly be viewed as imparting ones willpower/Haki to the air like a projectile.
Only Soru does not seem to fit this but Sanji's simular technique (Blue Walk) was (at least partially) transfered to Nami when his mind was transfered.  By this answer Haki is transferred but not physical strength.
There are several other techniques that, if these are Haki based, would also need to be Haki based such as Sanji's Sky and Blue walks and Zorro's ranged sword attacks.
Finally we address swordsmen. Not covered by the CP9's skill but still seems to be early stages of learning Haki is Zorro's cutting of steel.  His sword would normally not be able to cut something as hard or harder than itself but he learns to impart his willpower to it to make it cut what and only what he wants it to.  This is complemented by an early use of observation haki immediately prior to it in his fight against Mr. 1.
My one question is therefore: Are there any abilities that were shown prior to the introduction of haki on the show (such as the potential examples above) that have either been shown to work by using Busoshoku Haki (knowingly or not) after it's introduction or have been confirmed by canon sources to be Haki?
As I consider it Haki was introduced on Amazon Lily and in the several instances that were observed on the archipelago. The nature of this question invites speculation as I've done above but I would prefer justification in canon.  I understand anime physics don't have to be realistic but this would explain alot.

I'm sorry I don't really understand your question here, are you asking about what haki abilities that have been shown before the introduction of haki or after?

@ShinobuOshino Whether any bushido haki was shown before the archepelago arc where they feature it extensively to be explained partially on amazon lily. Not nessesarily connected to Rokushiki but that was listed as a case where we might have possibly seen it due to inherent simularilites between the abilities.

I don't think it was, apart from Garp hitting Luffy.

@PeterRaeves that's not haki, Oda said himself

Out of universe lore aside: We see Zorro use his (low-)ranged slash attack in the Punk Hazard arc when he cuts the snow-harpy in half. She is clearly shocked about the fact that she is still alive since had Zorro used Haki, her logia fruit would not have saved her. They are even talking about this afterwards and Zorro explains why he did not use Haki against her.

I will first use your examples to explain Rokushiki and Haki and then give a comparative conclusion using the wiki.
Rokushiki
Rokushiki was mainly explained in chapter 348 and was explained to be pure body strength with every technique. Rob Lucci confirms this after the CP9 had defeated the Strawhats for the first time.

Tekkai

Our bodies are trained to the point of mimicking an iron shell.

Soru

It only seems as though I've disappeared. With the explosive power of my legs...

Geppo (See also this question

(Also with the explosive power of my legs) I can kick the air and float...

Rankyaku

Nami: They cut the wall with their kicks!?
  Kalifa: If you have the speed to create a kamakaze, then it's possible...

Overall

We've trained our bodies to great extremes since we were young.

Strawhat crew's attacks

Sanji's sky and blue walk are basically like Geppo. The more power you gain in your legs, the faster you can move. So if you master this technique anyone could do it, as we have seen Sanji do in Nami's body. This could be argued to only have been possible by Sanji somehow imbuing Haki into Nami's legs as she would not have been as powerful to use blue walk. That's why I mentioned that technique is needed also. After being a thief and being on the run for most of her teen years, Nami has the physical potential of using blue and maybe even sky walk, she just didn't learn the technique needed to do so.
Zoro's ranged attacks are basically like Rankyaku. The more speed you can put in your slashes, the bigger the slash gets. Haki can be imbued to make the slash stronger as Law did against Vergo or when Mihawk slashed at Whitebeard (the fact whether Haki was imbued here, is debatable though). Haki can be imbued, but it isn't needed to create ranged slashes as explained with Rankyaku. Mere arm power or slash techniques would be enough.
Zoro cutting steel aka Mr.1
As explained in the following question, Zoro did not use haki in Alabasta

Haki
Haki on the other hand is a pure mental power and it might not even be possible to get it out even with enormous training.

Overall

Haki is a power that lies dormant in all the world's creatures, but a majority of humans go without noticing this power or perhaps finish their lives failing to ever pull it out, even if they try...

Kenbunshoku Haki

The ability to sense the opponent's presence even more strongly is haki with the color of observation.

Busoshoku Haki

This power can also be imbued into weapons (and can thus not be a mere physical trait as you can't train weapons)

Haoshoku Haki

This color of the conquerer however, cannot be trained and strengthened, even if you are able to control it.

Difference
Therefore to conclude, Rokushiki is not Haki. The result might be similar, but they are fundamentally different. Rokushiki is based on pure physical power, while Haki is based on will power. You could therefore technically have both Rokushiki Tekkai enhancement and Busoshuoku Haki at the same time, although this has not been shown in the series thus far. This is also why Rokushiki can be easily taught by becoming physically stronger, while Haki must be developed by becoming mentally stronger, which isn't as easy to do. Rokushiki will therefore not make the user able to negate Devil Fruit powers and hit Logia users for example.

Tekkai is similar to Busoshoku Haki, as both reinforce the users body in some way, the difference being that Haki is based on the user's willpower and Tekkai is based on the user's physical power. Also, Tekkai is more inclined to defense and the user exhibits no movement while it is active. In comparison, Busoshoku Haki is capable of both offense and defense.

Source on Tekkai

Other information
If you want to read more about Haki, see the question about the abilities that are transferred when hearts are interchanged between bodies
If you want to read more about Geppo, see the question about how CP9 members and Sanji can run in the air
Usage
Background

It was used by Garp for the first time against Luffy to bypass his Devil Fruit power and hurt him in Water 7. Later, Sentomaru used a Haki-imbued attack against Luffy, which made the Straw Hats think he was a Devil Fruit user due to their lack of knowledge about the ability. Afterwards, Rayleigh used Haki to stop Kizaru and even touch his Logia body. The first time the Kujas named this ability "Haki", they were shown wielding Haki-imbued arrows. During the Marineford War, Haki was also used many times by marines and pirates alike. It was shown that Haki is very common in the New World, unlike in Paradise where Haki users are fairly rare and almost nobody knows about it. It is later explained by Rayleigh once he begins training Luffy.

Examples

It can be used to augment the user's own attacks, projected ahead of the user as pure brute force, or imbued in weapons to increase their effectiveness. Any attack enhanced by Busoshoku Haki hits immensely harder than it would normally be without it. The Kuja's Haki-imbued arrows, for example, are capable of penetrating solid stone.
This type of Haki also has the ability to bypass the powers of a Devil Fruit user, touching the "substantial body" beneath whatever protection the fruit provides, such as the case of body-altering Devil Fruits such as Logia or Paramecia users. However, unlike Kairoseki, it does not negate a user's Devil Fruit powers, allowing them to defend themselves, and continue fighting normally. By the same effect, this Haki can also be used as a higher level of offensive, more so than just bypassing a foe's Devil Fruit powers.
A heavy concentration (or coating) of this Haki can be used to harden parts of one's body, turning the area black, thus making the user denser and more formidable, and giving their attacks greater power. Although Luffy, the first in the mainstream storyline to demonstrate this effect, named the technique as Busoshoku: Koka (武装色 硬化 Busō-shoku: Kōka?, Color of Armaments: Hardening), no other users except Donquixote Doflamingo, such as Vergo and Smoker referred to this method by such a name.
Busoshoku Haki works independently of the user's Devil Fruit, as shown when Luffy uses it to enhance his Gear Third attack underwater. This type of Haki may not be equipped to attacks that are not from one's body except for weapons, or anything generated from one's own body (like Kizaru's laser beams, Marco's flames or any other energy/non-solid attacks based on Devil Fruits). So, those who attack with parts of their body can combine their Haki and Devil Fruit powers.

Source on Busoshoku Haki

I don't consider the wiki a Canon source as I could edit it now to say it is haki.  That doesn't, however, mean you are wrong (which is why I asked). Vergo may be your combined haki and Rokushiki user at the same time but it isnt stated. I remember his shigan turning black but need to find that.

Ah! His shigan being black may have been his gloves in the manga as I cant find an image from the anime.

@kaine I just checked, but at the time Vergo attacked G5 it looked like he was wearing black gloves. So it's hard to tell whether he used Haki. I doubt he did, because he wouldn't really need it against fodder.

@kaine He is wearing gloves, check this out. https://i.sstatic.net/wsMOp.png

TL;DR: "Garp for the first time against Luffy to bypass his Devil Fruit power and hurt him in Water 7. Later, Sentomaru used a Haki-imbued attack against Luffy, which made the Straw Hats think he was a Devil Fruit user due to their lack of knowledge about the ability. Afterwards, Rayleigh used Haki to stop Kizaru and even touch his Logia body. The first time the Kujas named this ability "Haki", they were shown wielding Haki-imbued arrows. During the Marineford War, Haki was also used many times by marines and pirates alike." -- for Busoshoku Haki

@DazC i know this answer has gotten way too long but did u just copy random text from the answer? The real tl;dr is "haki is will power. Rokushiki is physical power". Maybe i should start adding tl;dr's to my answers.

The question asks for prior skills/abilities so I picked out prior instances/displays (Garp's punch, Sentomaru's push, Rayleigh's kick, Kuja's arrows, war soldier's war soldiering) from Paradise.

@DazC I guess all prior busoshoku haki usage was all remembered when rayleigh explained haki to luffy. Basically all those u said. I should really revise this answer some time in the future.

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Luffy as a water balloon
We discussed a lot about drowning devil fruit users in a bath - see this question: Can a Devil Fruit user drown in a bathtub?.
So now I remembered the fight between Luffy and Crocodile. To have a chance, Luffy drank a lot of water and was like a water ballon. But why didn't this affect his strength?
Does he have to be surrounded by water?

I think he isn't affected, because technically at that time, he isn't submerged in water, but the water is rather submerged within him. According to the rule, this should be fine. If it wasn't, Devil Fruit Users would always die of thirst or even die from the water within their own body. This type of water could also be considered "moving" water, as it moves constantly with every move you make. The same goes for when Luffy defended Whitebeard against Crocodile at Marineford. At that time he covered himself with water and was still able to move freely, since it would be considered moving water. So unless they are submerged into it, Devil Fruit users can touch water without weakening.
From the Devil Fruit wiki page.

With this new power comes a weakness: the sea rejects the new Devil Fruit user and they become helpless while submerged in water (or "become a hammer," in Japanese parlance).[2] Oda stated in SBS that Devil Fruit users are susceptible to all types of water, not just seawater. This includes the white sea surrounding Skypiea. He elaborated on this, saying that "moving" water, like rain or waves, does not weaken Devil Fruit users, while standing water does.

But they don't have to be completely submerged right? In arlong park luffy is submerged except his head. he still doesn't get his strength back seeing as he needs to resuscitated and the water needs to be pumped out of him

@Wouter No, a little submersion already drains his energy (eg: when Luffy fell in the well (in the shortcut) in Dressrosa, when he put his hand in the sea at the Fishman arc to save Sanji or attack that fishman). There has been one exception, but as I said there, that was just a fanservice moment, instead of an actual loophole.

I had the notion that devil fruit users have to be weary sea water, not just any water. That's why Luffy's power didn't work when an enemy put him into a prison made of sea stone.

My guess is that it was sweet water. Whereas sea water takes away powers, not just any water. He must be ok with swimming pools too.
P.S. There was a question about salt too. But I don't think we should seek deep logic here. Sea and seastone annihilates devil fruits power. simple as that. :) Unless Oda sensei decides that some other staff being dangerous will help the plot rolling.

Then what about when Luffy attacked Crocodile at Marineford? Since there wasn't much other water around,  didn't he use seawater at that point?

I am sure there was some sweatwater supplies there too. But as I said - don't read too much into it.

Unfortunately you made the same mistake I always did.  It is any water... no just salt water.  This was from a statement by Oda.


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Are anime that air before a manga adaptation considered filler anime?
In the question Has an anime ever come out before the manga was published? it became quite obvious that there are indeed several animes that air before their manga has been made.
But this also made me wonder about the following: Does this imply that all anime that air before a manga of it exist should be considered fillers?
Fillers are non-canonical material, which usually implies it did not happen in the manga. Or as Urban Dictionary stated it

filler
A segment of anime, whether it be an entire episode or part of one, which does not appear in the manga of the title. Fillers, as the name implies, "fills" an episode with non-canonical material which has been written usually by the same company which animates it.

I feel there's a bit of misconception here.

Fillers == Not canon
Canon == Original material from the original author.

There are episodes in Naruto for example, (like Naruto episode 101) which are canon but were not in the manga.
So the question of whether content being filler or not has nothing to do with it being in one medium or another (although there's usually a correlation). It's about who made it.

But episode 101 to 106 are considered fillers. Which is why it confuses me.

They are not fillers. They are canon episodes which were not featured in the manga.

Coming from this question. What about filler anime, that is original material from the original author (eg: Most of the episodes of dragon ball super thusfar)?

@PeterRaeves Read again, Canon == Original material from the original author.

I take "filler episodes" to be episodes that are side-stories that actively avoid making any significant changes to the overall story, in order to extend the length of the series.
There are anime series which opted to instead finish the overall story their own way, rather  than use what I would call filler episodes to wait for the manga series to get ahead.  Though this is not the canon the original author made up, I would not consider these filler episodes, but rather an alternate canon.
Two series I know of that have done this are Full Metal Alchemist (not Brotherhood), and Full Moon wo Sagashite.
It seems to me a silly definition to call anything non-canon according to the original manga author "filler", since most people talk about filler episodes in the context of those episodes that may be skipped, or are less interesting because they are obviously avoiding advancing the overall plot.  Plus, the original definition of the word seems to imply to me that the fandom definition has this meaning.
I might even consider an episode that is canon even in the original manga to be filler, if it seems that it's being used to extend the length of the series without really accomplishing anything meaningful.


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Why doesn't Infinite Tsukuyomi work on Tobirama Senju?
Manga Spoiler Alert
In the latest manga chapter (677), Madara successfully initiated the Infinite Tsukuyomi.
However, Tobirama Senju seems to be unaffected by this. Why is that?
See reference image below:

Given the fact that none of the Edo Tensei'd Hokages were affected, I'm guessing that Edo Tensei reanimated people are not affected by it.
There wasn't much said about it anyway, but that's the option that makes most sense.

I agree with Madara Uchicha's answer, the dead (Edo Tensei'd) characters don't have original chakra for the God Tree, so the the tree does not attempt to absorb them?
Maybe the Hokages will help Naruto and Sasuke attack Madara.

It seems to me the God Tree and Infinite Tsukuyomi targets bodies with life force and chakra.  Edo Tensei shinobi possesses infinite chakra, but not any life force, which is insufficient to fall under the genjutsu.
Beyond this, Kishimoto has never shown any Edo Tensei falling under genjutsu. Furthermore, when Sasuke (from Sasuke Retsuden) tries to put Meno (an Edo Tensei dragon) in a genjutsu, it doesn't work.

Edo Tensei reanimations have been shown to be put under genjutsu: namely, Itachi Uchiha is affected by Kotoamatsukami in chapter 550.


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Did Kakashi's sharingan evolve because Obito was watching?
Both Kakashi and Obito awaken their Mangekyou at the same time as told in this question When did Kakashi and Obito awaken their Mangekyou Sharingan?  The sharingan Kakashi owns originally came from Obito, so is it due to Obito also being there at the moment Rin died that Kakashi's Mangekyou also awakend? Or asked in a different way. Would Kakashi have been able to awaken the Mangekyou without Obito being there?

Interesting question with no definite answer, so I'll post my 2c here.
The Mangekyou Sharingan is activated by the immense grief caused by killing the person closest to you. However, it seems like you don't actually have to kill him, but witnessing his death is enough.
For example, Itachi did not actually kill Shisui, rather, he watched him commit suicide (filler).
I believe that both of them awakened their Mangekyou Sharingans separately, and because they were both at the scene when it happened, it happened simultaneously.

So its pretty safe to assume that if one of them was not there, that person would not off awakend the mangekyou?

@Dimitrimx I'm pretty sure the other person would still awaken the Mangekyou because if you remeber correctly, Obito was kind of seeing what Kakashi was seeing before he got to where he was (he was seeing small scenes of Rin dying).

Just a note: there are different versions of Shisui's death. In the Itachi light novels, Shisui tells Itachi to kill him so he can get his Mangekyou. Itachi pushes him in this version. The light novels are adapted in the anime, but I haven't seen them, so I don't know what that arc has to say about these events.

The Sharingan was stated to be the result of special chakra inside a Uchiha's brain altering their optic nerve when they lose those they love as Kakashi is not a Uchiha he is unlikely to be able to produce the special chakra required to gain the Mangekyou Sharingan.
Obito could still see through Kakashi's Sharingan when in close proximity had showing he is still connected to the Sharingan he gave Kakashi so I believe that through that connection the special chakra produced in Obito brain evolving his Sharingan into the Mangekyou Sharingan was trasfered to Kakashi's Sharingan causing it to evolve into the Mangekyou Sharingan.

And where might this be stated? with some valid sources this would be a amazing answer.

I seem to remember something like this being stated too. It might have been in Kakashi: Shadow of the Anbu Black Ops, or it might have been in the Itachi light novels. Or in a recent episode that aired in the US on Toonami.

Both awoke mangekyou at the same time but only obito is aware of it and can use it. It took kakashi much longer to recognise its existence and convert it to a usable ninjutsu.

The visual prowess of the eye does not depend on the will of the person using it but on the one to whom it originally belongs to (because of Madara using his brother's visual prowess and even Sasuke using Itachi's visual prowess without originally having the abilities. Also, Itachi used Shisui's visual prowess without having Kotoamatsukami originally). Therefore, Kakashi did not awaken the Mangekyou. It was Obito who awakened it in both eyes.


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Where does the shroom on the head come from?
If been re-watching some Gintama episodes and noticed the parasitic mushrooms in some episode. Which started to grow on their head and slowly take them over.
I also came across the pokemon Paras to which something pretty similar happens:

While Paras' symbiotic relationship with the mushrooms on its back isn't exactly normal, it is beneficial for both; Paras feeds the mushrooms with its body, and the fungus provides additional means of defense. Exactly how much control the mushrooms can exert over the Pokemon isn't clear, but odd goes to disturbing when Paras evolves into Parasect.
It's hard to say exactly what change takes place at Level 24, but for some reason, the mushrooms take their chance and merge into a single organism, taking over the Paras in the process. With heightened aggression and a pair of zombified milky eyes, anything cute or endearing about Paras is replaced by a demonic drone known as Parasect.

So now my question: where does the parasitic mushroom come from? Is this made up in anime, or like allot of other anime components based on some kind of folk lore?

Related? http://anime.stackexchange.com/questions/7530/what-is-the-origin-of-mushrooms-growing-on-a-sad-persons-head

@Memor-X Don't think so, but wont know unless somebody answers ;P

if your question is about parasitic fungus then this might be of help just from reading about Parasect, particular how Cordyceps is used in The Last of Us, i haven't seen Gintama so i can't tell if the mushroom thing is a gag or not

It is also in Fairy Tail
i dont have anything left to say!

I don't think that Gintama, Pokemon and trope head mushrooms are related.
The reasons for each seem to be entirely different. Parasitic mushrooms exist in real world and that's where most of Pokemon character design inspiration comes from. Gintama is an adventure where a "parasite infection" would be a nice plot point for a story to evolve around, and the "sad mushroom" trope doesn't seem to be involved in either.

The parasitic mushroom comes from real life. Cordyceps

From http://i.guim.co.uk/static/w-620/h--/q-95/sys-images/Guardian/Pix/pictures/2012/5/3/1336047375506/Zombie-ant-infected-with--001.jpg
This fungus infects insect and uses them to breed. This is where Game Freak got its inspiration for Parasect.


text:
How many chapter are stocked by publishers?
I was wondering if every mangaka (or prehaps most of them) prepares some chapter beforehand, or if they develop the plot and draw the chapter at a glance, during the week after the last one is released.
I red this question and the answer with lowest score is very nice, but without a link is not possible to define it credible (with respect of the author).
Maybe Shonen Jump (and other magazine) require an amount of chapters beforehand, in order to be "safe" in case of something happens?

As the answer in the previous question said, mangakas are ahead of 3-4 chapters though this figure may vary in some cases. The credible source for this is Eiichiro Oda, creator of One Piece manga, answers his fans questions at the SBS Corner, here's what he had said about this in particular:

D: When an artist is drawing for example, Chapter 10, what chapter is
being printed in the newest Weekly Jump?
O: I see. I wondered about
this myself, years ago. So I understand your curiosity. At this EXACT
moment, Issue 46 of Jump is hitting the stands. It contains One Piece
Chapter 60, "Solution". But I have finished the drafts up through
Chapter 63, "I Ain't Gonna Die". So a chapter comes out roughly 3
weeks after I finish it. But that's only my CURRENT schedule. Not all
people drawing weekly serials have the same system. I could change if
need be. There are various cases.Source

And for your other question of how far ahead the mangaka develops the plot, Hiro Mashima, the mangaka of Fairy Tail says:

Q: How far in advance do you create your stories (before they're
published in Shonen Magazine)?
Hiro Mashima: Generally speaking, I tend to think of the next episode
as I'm creating the current one. Sometimes I get writers block.
Sometimes inspiration just comes when you're sitting down at the
toilet. I like to think of that as just an inspiration from heaven.
(laughs)
Source

Other references:

Yahoo answers
Insight on how mangas are created and typical schedule of mangakas

@JaAd You're welcome desu~

This answer (generally) also applies to just about every form of serialized entertainment: TV shows, newspaper comics, etc. The writer(s)/artist(s)/actor(s)/etc. create serials in advance of what's available to the public. How far in advance depends on the media and production group/individual in question, but it happens everywhere.

@BrianS i agree. I thought that mangaka are from another universe, especially Oda ;-) .


text:
Why did Nadeko use different names for Araragi?
Episode 12, the story about Otorimonogatari, contains the story Nadeko Medusa. Nadeko said this:

Favorite big brother: Koyomi Oniichan
In Love with: Araragi Koyomi

why she said it differently? Does it mean that she consider Araragi as two different person? Because in Monogatari Series Second Season she turn out to be a

 yandere, and want to kill Araragi, the man that she love.

…Or, or! It could just be that it sounded neater using two different ways to address Koyomi instead of repeating the same way twice in such an intense scene, so it wouldn't seem out of place.

The difference emphasizes the extent of her love towards Araragi: she loves Araragi as a big brother figure as much as she loves Araragi as a man.

Favorite big brother: Koyomi Oniichan

This is the love of a sister for her big brother. Sibling love.
The honorific onii-chan shows that she holds Araragi very dear and sees him as if he were her real big brother.

In Love with: Araragi Koyomi

This is the love of a girl for a boy. Boy-girl love.
The absence of honorific, which is a stark contrast to the previous line, shows that she loves Araragi as a member of opposite sex, not just love between sibling.

The Oniichan has nothing to do with who she is. Oniichan is the honorific used when addressing an older brother. If you'll see, it's listed as "favorite big brother" before referring to him as "oniichan".
You can check out this page for a full list of Japanese honorifics.


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Can a guild mark be forcefully applied?
The What exactly is a guild mark? question made me wonder about this aswell.
Can a guild mark be forcefully applied on somebody? Or is it a process of mutual acceptance. Or maybe even like with the celestial spirits, a contract?

i think as guild mark is required for some magic, no guild would forcefully apply on anyone to reveal their magic.

possible, I remember when Flare want to burn Lucy FT mark with Raven Tail mark, but I'm not really sure since she failed to do so

Gajeel, a former Phantom Lord member, joined Fairy Tail after the defeat of his former guild. Also,

Moved by Makarov's mercy and compassion, Gajeel accepts his offer.

Juvia, like Gajeel, was a former Phantom Lord member. She joined Fairy Tail after the defeat of her former guild.

Juvia goes to the newly renovated Fairy Tail guildhall to meet with
  the guild's master, Makarov Dreyar, now prepared to ask him for guild
  membership.

Lucy Also joins the guild on her own accord.
From the above examples, we can see that each character of the story joins the guild upon the mutual agreement of the Guild Master and him/herself.
Yukino, upon her loss she was forced to strip and asked to erase her guild mark, thus banishing her from the guild. She was very disappointed with this.

After failing to win, Yukino faces the anger of Sabertooth's Guild
  Master, Jiemma. Displeased by the failure of Team Sabertooth on the
  second day, Jiemma throws grapes at Yukino's head and forces her to
  strip, telling her to erase her guild mark, thus banishing her from
  the guild. She is later seen standing outside Honeybone Lodge, the
  current lodging of the Fairy Tail Guild for the duration of the games.

Laxus:

As he informs the Thunder God Tribe of his expulsion, Bickslow tries
  to convince him otherwise, but Laxus tells him not to take action.
  Laxus watches the Fantasia parade before he leaves and realizes that
  everyone, including his grandfather whom he despised, is still looking
  out for him. Laxus leaves the parade realizing what a fool he was,
  smiling but shedding tears of regret.

A member is excommunicated from the guild at the discretion of the Guild Master as we can see in case of Laxus and Yukino.
Also, as Sp0t mentions, no guild would forcefully apply on anyone their guild emblem to reveal their magic. When someone joins the guild, he/she is privy to the working of the guild and also some secrets. Why would a guild master force someone to join and out these critical information at risk? As we have seen that Gajeel was used to counter spy on Ivan which was devastating to the Raven Tail Guild.
So I would say that a member joins a guild with the mutual agreement of the Guild Master and him/herself.
P.S: there is always a possibility where a character is blackmailed to join a guild, but if we blind side the "blackmail" part we can say that he agreed to join the guild. The agreement may not be completely mutual, but nevertheless it's mutual (ugh... I know it's complex). But I doubt that such an agreement can be beneficial to the guild.


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How is Misaka's railgun so destructive?
In episode 1 of Railgun, Misaka's railgun up-ends a good chunk of what appears to be an olympic-sized swimming pool. Later in the same episode, it is revealed that her railgun travels at a velocity of 1030 m/s.

However, the numbers don't add up.
Suppose Misaka uses 10 gram coins. At 1030 m/s, that coin has this much energy:
Energy = 1/2 m v^2
       = 1/2 (0.01 kg) (1030 m/s)^2 = 5304.5 kg (m/s)^2
       = 5304.5 Joules

An olympic-sized swimming pool has 2,500,000 kg of water. Based on the image above, that cone probably travels a good 100 meters into the air.
So let's say for benefit of the doubt, that only 10% of the water is lifted 100 meters into the air.
Energy = m g h
       = (0.01 * 2500000 kg) (9.8 m/s^2) (100 m) = 2.45 * 10^8 kg (m/s)^2
       = 2.45 * 10^8 Joules

The coin needs 2.45 * 10^8 Joules of energy to uplift the swimming pool as shown above. But her coin can only provide 5304.5 Joules. There is a difference of about 4 orders of magnitude.

Okay... Before anyone dismisses this as just another case of Anime physics, let's look at what else could produce so much energy:

The spin of the coin is not captured in the net velocity of 1030 m/s. But given the moment of inertia of a little coin, it would need a tremendous (relativistic?) amount of spin to carry 10^8 Joules.
The charge of the coin is unspecified in the Anime. Perhaps Misaka somehow polarizes the charge in the coin and somehow makes it release upon contact with the target.
The mass-energy (E = mc^2) of the coin is 9 * 10^14 Joules. Is this what she did?

So the question is: Is there any official explanation for where the coin gets so much energy? Or are we left to dismiss this as another case of Anime physics?

And if anyone is interested in the chat discussion about the physics here: http://chat.stackexchange.com/transcript/message/7951592#7951592

FWIW, Funimation wrote a blog post, A Certain Scientific Explanation of Railguns, last year. Sadly, the linked PDF that ran the numbers and lampshaded how wrong it is appears to have been lost. IIRC, the answers here already cover everything it said anyway.

@Mystical by Official do you mean a purely physics explanation or a canonical explanation?

@Mindwin By "Official" I mean if the studio or any of the authors have said anything.

According to the anime and manga, Mikoto has a "muzzle velocity" of 1030 m/s:

In contrast, the US Navy's railgun has a muzzle velocity of 2520 m/s (~5600 mph or ~7.5x the speed of sound), with a muzzle energy of 10.64 megajoules (10.64 million joules). Which is probably comparable to the amount of energy in an average-sized car moving at 250 mph.
Comparatively, the an AK-47 rifle has a muzzle velocity of 715m/s (~1600 mph or ~2x the speed of sound), with a muzzle energy of ~2010 joules (assuming 7.62x39mm cartridges are used, but may vary depending on the type of ammunition).
While not very impressive stat-wise as far railguns go, since actual railguns are capable of achieving speeds of possibly more than ~5000 m/s. Take note that Mikoto is a middle-schooler that can fire eight shots of these per minute, which is on par with "typical" railguns.
Assuming the coin comparable to the size and weight of a U.S. quarter, one can assume that the coin she uses has a weight of about five grams. Using this formula we can get he muzzle energy:

Energy = 0.5*(mass)(velocity)2 = 0.5*(0.005kg)(1030m/s)2 = ~2652.25 joules

So Mikoto outputs a bit more damage than an semi-automatic assault rifle.
But that's not what we're seeing now is it?

Not quite. But what could cause such a difference in output?
According to Page 1, Chapter 4 of the Railgun manga, she manipulates electromagnetism to achieve her results. This seems plausible since if the magnetic field were sufficiently focused, she could theoretically accelerate only the coin and/or nearby objects.
Now lets take a look at the pool test again, from the pool cleaning episode (S1, ep. 2) we have an approximate estimate of the dimensions of the pool:

Lets measure things in terms of Kuroko's height (~152cm)!

Seeing as the pool doesn't taper or either end, lets assume that the pool is about 14 Kurokos long or ~21.28 m (yes it does seem kinda small), and about 11 Kurokos wide, or ~16.72 m, by the lines on the pool floor and a bit less than ~0.9 Kuroko, or lets say 1.36m deep.
As for the displaced water, we could attempt to integrate the volume of the plume of water, assuming it's half and half air, find it's weight, etc. But we'll be lazy here and assume that 1/1000th of the pool water volume was dispersed into the air when Mikoto fires her railgun. The pool would have a volume:

Volume = (1.36 m)*(21.28 m)*(16.72 m) = ~486.73 m3 of water

Since the "center of mass" the plume of water seems to be comparable be near the top of the gymnasium-type building, going be an eye estimate of the door compared to the building lets assume that it's 10 m tall. In order to calculate the energy needed to achieve something like this we do:

(Energy it takes to lift an object) = (mass of object)*(acceleration due to gravity)*(lift altitude).

In this scenario let us cut a bunch of corners and assume that all the energy of the shot goes into lifting the water (by which ignore the energy spent warming the water up, creating the sounds loud explosion, any dramatic winds effect), then we have

Energy = (1/1000)*(~486.73 m3)*(1000 kg/m3 water)*(9.8 m/s2)*(10m) = ~47699.54 joules

If we plug it backwards into the kinetic energy equation:

√[(~47699.54 J)*2 / (0.005 kg)] = ~4368.04 m/s

So the muzzle velocity of her railgun would be ~4368.04 m/s.
One can only assume that, since we must respect the canon value of 1030 m/s, that perhaps the damage caused by Mikoto ability is due to her manipulation of electromagnetic caused as the coin moves through the air or some other factor... But then again, what do we know about the physics of this world where Science and Magic co-exist?

@Krazer by the looks of it, seems like a semi-olympic pool, 25m x 12.5m x 1.36m

Electricity can move the water:
The wiki says that Misaka can generate 1 billion volts.
(even though some sources states 5 billion volts, lets be MODEST <grin>)
If she charges the coin, the rapid transfer of charge from the coin to the water would cause repulsion between the coin and the surrounding water, propelling the water away from the pool. The shockwaves would reflect on the borders and the bottom of the pool, pushing the surface water up.
You can see in the anime that all the blasts have some sideways movement, but the SECOND blast displayed has a very distinctive. sideways movement, hinting that the impact pushes the water a bit to the sides as well, as the electrically charged water moves away from the coin while the coin traverses the pool.
The issue of the charge dissipating is not a problem. She can AIM lightning, so we can assume her electromagnetic powers can also alter the breakdown voltage of the air around the coin (by either increasing the pressure around coin or making vacuum.
We need to look at the capacitance of the coin

The radius of a quarter is 13mm

With a potential of 1 billion volts, the charge of the coin is

Now, We can calculate the electric force between the charged coin and the charged water, and for brevity's sake, lets assume:

half the charge has transferred to the water.
the walls and bottom of the swimming pool are totally isolant and indestructible.
the coin has hit the bottom once half the charge is transferred.
The water is 1mm away from the coin

In this situation, The force between coin and water is calculated with coulomb's law:

We are getting to the Megajoule Here.
Given the mass of 10% the pool's water, that force gives the water a momentary acceleration of:

Now, to lift the water 100 meters, we need to imprint the water a velocity of 44.3m/s

So the interaction time between coin and water before the remaining energy dissipates making:

Krazer said:
     energy spent warming the water up,
     creating the sounds loud explosion,
     any dramatic winds effect

And that's  that accounts for

Even if you were to take into account the charge dissipation, the diminishing repulsion force between the water, and other small assumptions here, there is plenty of energy for everything.
There is plenty of energy everywhere to be used any way you want.
But I think this clearly explains where the energy to lift the water comes from.
Also, if you take the events of later episodes, when she uses other items than a coin

 A giant robot claw and later on a whole giant robot

you can see that the amount of stored energy is greater, and so is the destructive power. Makes sense, because the capacitance of those items is bigger than a coin's.
Many thanks to Wolfram Alpha for the calculations and images.

More theories:
Electricity can keep accelerating the coin even after it left the "muzzle".
If she charges the coin, she can generate another charge of the same sign on herself after the coin leaves the "muzzle". So even if the coin leaves at a velocity of 1030m/s, she could accelerate it even after it was fired. But its not even necessary, because...
The coin's Spin and one of most destructive forces: Harmonics.
As we can see from this wikipedia graph, once maximum resonance (1:1) is reached, the energy transfer increases dramatically. Wind Harmonics are enough to destroy a bridge by moving it like a violin string. If she can spin the coin so its frequency matches perfectly the harmonic frequency of the pool, massive energy could be transfered.

I just noticed that the water would take 9 seconds to go up 100 meters at 44.3 m/s. Since the blast takes only a few frames, we can assume the contact time is a bit LONGER THAN 5ms, and the upward water just thins/evaporates after hitting 100m

Well, the pool is only one example, we often see her stop and blast cars up in the air, produce enough heat to melt two consecutive metal bars, and leave a deep scratch on the earth it travelled over, even without direct contact. It would seem as though there's another energy aside from the coin's sheer velocity.

Also not to mention that in the Railgun series, she shown that she can propel items other than a coin (namely, a giant robot arm and an entire satellite) to similar velocities.

While subjective, it was my strong impression from the start that projectile component is indirect (and possibly borderline irrelevant) to her ability.

She can produce a lot of energy
The energy goes where projectile goes
However, it is not established that the projectile carries the energy

The projectile might be just a beacon or focus type of component, possibly purely psychological one (with technique being opposite of just randomly shooting out bursts of uncontrolled electricity).
I remember her shooting large projectile in later episodes, however, the speculation above might still apply.

+1, this is a great explanation IMO. There might've been a scene where people find a coin of hers, but I recall that many firings of her railgun had the coin become a beam, I assume melting it in the process (if anything remains of it at all).

A way to verify this would be to see if she ever uses anything non-metal as the projectile. If her Railgun is actually a Railgun in the scientific sense, it would have to act on something that can be accelerated with electromagnetism, so a metal of some kind. If she can use non-metallic items, then its not actually a railgun and this explanation would be very convincing.

I argue that it is a case of Anime Physics by refuting the alternative possibilities you suggested.

You're right - carrying such an amount of energy as moment of inertia is impossible. Even Misaka's superpowers are a world away from relativistic speeds.
The energy cannot be stored as charge in the coin, as it would keep dissipating as "lightning".
The energy couldn't have come from mass energy. Besides the resulting lethal radiation, to release mass energy without using antimatter would mean releasing nuclear energy. Nuclear energy can only be released under extreme pressure (nuclear reactions in bombs are initiated by compressing Uranium with the blast of a smaller bomb). If someone could find an example of Misaka finding her coin after she shot it, that will clearly refute the mass energy argument.

Finally, the Mythbusters proved in this video that a coin travelling at 3 times the speed of sound (around the speed of a bullet) merely dents concrete.

It is also worth noting that (insofar as I recall) the 'psychic' powers of the type Misaka has are loosely based on the ever-popular, fantastic, double-misinterpretation of the Schrödinger's-cat thought experiment: that perception influences reality, and thus altering perception in the correct manner should alter reality. (Or something like that. There was surrounding techno-babble, but that seemed to be the gist of it.)
Thus, an alternate though less-interesting explanation of the disproportionate effects of her railgun would be something along the lines of: Misaka's own perception of how powerful the railgun should be is wrong, resulting in exaggerated effects.

You guys are all forgetting the basic fact that the 1030 m/s measurement was taken while firing into water. The effects of drag on the coin fired into water are far greater in magnitude than the effects of drag while fired through air. Air is almost one thousand times less dense than water. If we perform the equation for drag, we come up with a force magnitude on the coin of 18,466 Newtons. [18466=.5*1000kg/m^3*(1030m/s)^2*.82*0.000042455m^2]
.82 is the drag coefficient for a long cylinder like an arcade coin, 1000kg/m^3 is the density of water, and .000042455m^2 is the cross sectional area of the coin fired.
if we perform the equation in reverse to find out the velocity of the coin in air, we are left with a velocity of 29,428m/s.
Sounds a hell of a lot more like a proper rail gun, doesn't it?

'A Certain Magical Index' has 50 odd light novels, 13 volumes of manga, 2 seasons of anime, a movie and a couple of video games.
'A Certain Scientific Railgun' has 2 light novels, 11 volumes of manga, 2 seasons of anime, an OVA, and a video game of its own.
In none of these sources (that I can recall, anyway) is Misaka's railgun trick implied to be anything other than an arcade token (not a coin, which is why it is even ferrous to begin with) travelling three times the speed of sound.
And there is one other weird property of the railgun attack - Touma, the boy with the anti-magic fist, can catch it. (As seen in chapter 7, volume 1 of the Railgun manga.)
Since Touma can dispel it, that means that there is still something supernatural about the coin, even while it is melting. That supernatural property will be why it has a pushing force well above what it should have on momentum alone.
I have no evidence for my next point, but I believe that Misaka's magnetic field is simply continuing to push the coin well after it leaves her hand. That would explain both oddities nicely.

Let's not forget in the episode she did the robot arm she did so because the person was sitting outside the range of her coins. At the end of the beam there was simply no coin left. She explained as she blocked, caught, and fired said arm that there is a reason she usually uses coins.
I suspect several factors combine to contribute to her destructive potential including her designated badass status, continued acceleration, inertia, spin, hypersonic shockwave, and possible conversion of matter to plasma.
Remember she also probably diverting energy to fight recoil and other destructive aspects of firing the railgun. That shielding is sufficient to stop directed multiple nuclear blasts capable of rapidly melting through concrete and steel despite Misaka being exhausted at the time. I'm sure this might be sufficient energy cause a secondary acceleration.

It is a case of anime physics as other posters have alluded to but not your average anime physics, it is said in certain parts of the manga and the sister series index that the way esper powers work is by manipulating a reality warping field to fit the style of their powers. therefore misaka's railgun works because it has sufficient reality warping energy and math behind it

It would be great if you could cite the exact chapter where that is mentioned.


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Which episodes of Fairy Tail are anime-exclusive?
Up to episode 175, I know Fairy Tail has some episodes which are not in the manga.
If I want to watch the series again but not the episodes that are anime-exclusive, which ones should I skip?
This question is inspired by Which episodes of Bleach are fillers, I just decided to do the same for Fairy Tail

These following episodes list the content which are only present in the anime of Fairy Tail, not in the manga.
This is a list of episodes defined as anime exclusive in the Fairy Tail Wikia
Compactly, it gives episodes: 19, 69-72, 74-75, 125-150, 204-218, 221, 223-225
Galuna Island Arc

Episode 19 - Challenging!

Daphne Arc

Episode 69 - Call of the Dragon
Episode 70 - Natsu Vs. Gray!!
Episode 71 - Friendship Will Overcome the Dead
Episode 72 - Fairy Tail Wizards
Episode 74 - Wendy's First Big Mission?!
Episode 75 - The 24-Hours Endurance Road Race

Key of the Starry Sky Arc

Episodes 125-150 - This whole arc is anime exclusive

Eclipse Celestial Spirits Arc

Episodes 204-218 - Stake My Life on Hospitality - Believe
Episode 221 - The White Silver Labyrinth
Episode 223 - Kemokemo Arrived!
Episode 224 - The Place You Came Before
Episode 225 - The Thunder Man

The series currently ends with Episode 235

According to that wiki page episode 19 is a filler episode within a canon arc.


text:
Which devil fruit is this, and what happend to it?
During the punk hazard arc we can see one of the apples in the sleigh transform into a devil fruit just before smiley turns every thing in to a deadly gaseous goo.
What happened to this devil fruit afterwards, and which devil fruit is it to begin with. Is it ever shown?

Since the marines go back to get their crew mates, i assume they would have acquired the fruit too! Nothing is shown as of now :)

I guess this question is related to your first question. When Smiley died and the Devil was released, he reincarnated into the apple. Aside from that, anybody's guess is as good as yours as to what happened to it. Caesar intended to recreate Smiley with it, but he never got the chance to go and get it.

I can only answer this question partially because of the information we currently have on One Piece.
The name of the Devil Fruit is: Sara Sara no Mi, Model: Axolotl.
If you wanna look up the name, it can be found in chapter 673, page 12.
As for what happened to the Devil Fruit, I have no clue since neither the manga nor the anime have shown/hinted at it being transported afterwards. So it might as well still be on Punk Hazard.

Because Smiley died the fruit was re-circulated,
you know how vegapunk was able to give inanimate objects the powers of a devil fruit, Caesar Clown did the same for smiley

This happend just before Smiley turned everything into a deadly gaseous goo. Aka just before he died. Do you maybe have some source material to back this statement up?


text:
Is sound genjutsu more powerful than eye genjutsu?
After going through this link, I came to a belief that sound genjutsu is far more superior to eye genjutsu.
After recalling the incident of the two Sage Toads' genjutsu and Kabuto's genjutsu, I felt that it was difficult for the Sharingan/Rinnegan users to concentrate on their battle.
So is my speculation true?
Some of the sound genjutsu techniques are listed here:

Demonic Illusion: Toad Confrontation Chant
Temple of Nirvana Technique
Demonic Flute:Phantom Sound Chains

It's not that sound genjutsu is superior. Sound genjutsu operates on a different sense, so that renders doujutsu (eye techniques) useless to escape from it, unlike with illusions that work on vision.
That makes sound based genjutsu more effective on Sharingan users, because they rely on their improved vision powers to counter most genjutsu.

The sound base genjutsu  can be more effective than eye contact base genjutsu cause we have seen might guy fighting itachi without looking into his eyes and no eye contact means no genjutsu but if sound base genjutsu is being used even a skilled opponents can not block or doge the sound waves completely plus its a sound base genjutsu so it depends on the air so it covers most of the effective areas.
Sound base genjutsu are really powerful but some of them cannot be performed simultaneously so this is disadvantage you have 1 shot if you miss that's all.
So in all manners and looking at the all points we can say that there are advantages and disadvantages of eye contact base genjutsu and sound base genjutsu.
That's what I think.

Going off of Madara's answer, sound and smell, maybe taste genjutsu would be most effective, since it doesn't affect the eyes but rather other senses, of which no doujutsu provides advantage to. If Madara were to be blinded, he would still be able to use doujutsu, but his other senses would diminish. This is a time when Orochimaru would come with something useful as he is the Sound Village's leader.

can u site some smell and taste genjutsu?

@Jiraiya As far as I know, there haven't been any mentioned or seen in the story. But in theory, if there is visual and sonic genjutsu, then there is most likely smell and taste variation. It's not too inconceivable, as it would be most effective to an opponent, considering a person may be deaf and blind, but everybody must breathe (except the dead of course). There's only so long a person can hold their breath, before succumbing to their body functions to passively breathe again.

your speculation is correct....no doubt about that but since we are dealing with this particular anime,i was expecting some facts with your statement.....no doubt about ur theory,but i was more intersted on the impact it might have against eye techniques

A ninja from one of the Naruto the movies was using a smell based genjutsu. I forget who. Her jutsu involves petal whirls.


text:
What is this bird?
In Hana-Saku Iroha there's always a big bird that appear

At first I thought it's like a god or something, but as far as I know it didn't do anything. What is this bird? and what is its role?

...it's just a bird (specifically, a Grey Heron / aosagi). Its role is being a bird. This is what most birds do.

@senshin well, most bird didn't interact with any character in almost every episode...

Its a common Dutch bird called Reiger from the Ardeidae family also called Grey Heron in english.
Their most common recognition points are

Blue/grayish back
White Belly
Long and sturdy beaks
A long neck that gets subtrackd in flight
From head to chest there is a long black stroke
Black strokes on the forehead of the bird
On his hind side there are some gracefull black feathers

EDIT
The episode is called Grey Heron Rhapsody, considering the meaning of Rhapsody

an effusively enthusiastic or ecstatic expression of feeling.

It would most likely mean the author expresses his feelings about the animal.

and what is it doing in anime? is it just for some funny moment? or maybe there's something behind it?

@ShinobuOshino Sorry, overlooked that part of the question. Edited my answer. Hope it is satisfactionary.

Grey Herons are common around Japan, especially in the rural country side where this story is taking place. Ohana is not use to seeing one in the wild, outside of a zoo.


text:
Can someone learn more than one alchemy?
In Fullmetal Alchemist: Brotherhood, the characters gain skill in alchemy through learning. So I'm wondering, is it possible to learn more than one alchemy? Because it seems like everyone is a specialized in particular alchemy. Also, if this possible, can they perform more than one alchemy at the same time?

Dude, that's, like, four whole alchemies!

Yes! Absolutely, characters can learn more than one kind of alchemy. It's just that, as in real life, people tend to specialize in something very specific and get very good at it.
But let's take a look at a few examples:

Edward Elric: Like Alphonse, he takes after Izumi Curtis's style (including the big fists and such), but was able to attempt Human Transmutation, soul binding, modification of object structures (such as what he did in Youswell or in Greed), and even weird, quirky things like transforming a military vehicle into a clown car.
Roy Mustang: Specializes in flame alchemy, but is seen, most obviously at the end of the series, to be able to modify structures of objects (when he makes a wall out of the ground). To do this prior to his "accident", he would have had to draw the transmutation circle, which is obviously less effective.
Tim Marcoh: Specializes in medicinal alchemy, but did so even before he began to specialize in the creation and destruction of Philosopher's Stones.
Scar: Is able to perform both destruction and creation alchemy through different transmutation arrays.

Then there's a few oddballs, but the rule can still apply to them:

Van Hohenheim: Specializes in medicinal alchemy, but is also seen modifying object structures including metal and stone.
Father: Can do pretty much everything, even before the climax; he is able to make homunculi, reshape metal, etc.

Keep in mind that, similar to what @kaine said, transmutation circles come into play. Not just in knowledge, though; the person actually has to either have that transmutation circle with them or draw it on the spot, which is not feasible in combat. So, someone like Armstrong would not thrive at the same things as Basque Grand, because they both use different transmutation circles. This is clear with Mustang who broadens his use of alchemy after his "accident".
So from this, we can tell that it's possible for alchemists to learn more than one type of alchemy, but it's difficult for them to always apply it under pressure (for multiple reasons); given cases like Ed, who doesn't need transmutation circles, we can see a broader range of alchemy used.

So..can they use more than one alchemy at the same time? Or somehow combine them?

@ShinobuOshino I don't see why not. Ed performs numerous types of alchemy when transforming that clown car, I don't see why someone with knowledge of, for example, water and freezing alchemy couldn't make grand statues of ice.

Also to add to this they all eventually switch to the eastern style at the end of brotherhood when Father switches off the energy from the mantle though you can argue they are still producing the same effects as before.

@Quikstryke That's not true. Western style uses tectonic energy, which was blocked by Father prior to the end of the series. After this blockage stopped, the Westerners went back to using tectonic energy. There is no suggestion that the "dragon's pulse" of the East is in any way the same as this.

Ah you are right about the battle. But doesnt negate the fact you cant use both which is essentially what scar's brother's research is on.  Al also heads east in the hopes of trying to learn and incorporate it to restore his brother.

Focusing on Edward, he does alchemy (at least) on metal, binds souls to armor, attempts human transmutation, repairs machines, changes carbon structure (in Greed), etc.
I believe that he does alchemy on what he feels useful. Everyone else is only limited by what circles they have already drawn (as they need transmutation circles to do alchemy) and their knowledge. In other words, they need to know the characteristics and how to draw the circles for what they are transmuting and what they are transmuting it from.  For instance Mustang handles fire as that is what transmutation circle is on his gloves.
TLDR: No, they are not (usually) only limited to one type of transmutation but they have to have the circle and knowledge for any transmutation they are doing.

can they use more than one alchemy at the same time? Or somehow combine them? also, do one circle is just for one alchemy?


text:
Nagato's Eye in Edo tensei Mode
After seeing this discussion here, I think how come Edo-tensei nagato had rinnegan. Nagato's original eyes were normal. He received rinnegan from madara. So his edo tensei form should have had normal eyes not rinnegan, if edo tensei brings the original soul; because his eyes were normal until madara gave him his rinnegan.

I think when a person is brought back by Edo Tensei, that person is revived from the last "checkpoint" of his life, when they were at their strongest. Even if originally Nagato's eyes weren't the Rinnegan, when he died he possessed it, similar to Itachi having a full potential Mangekyo Sharingan, yet he was blinded prior to his death in the last moment of his fight with Sasuke.
Since no other Uchiha was resurrected, nor other Rinnegan user was revived, this could be the only possible conclusion you can deduct from these shinobi (if you don't calculate to be a plot hole), that you're coming back from the time when you had your full strength. For example, look at Madara: he is in his younger ages, not an old grandpa who was shown in the cave with Obito.

But then, how would explain Madara's revival possessing Rinnegan? He only got those eyes when he was quite old.

kinda' combination of the best age with the best skills maybe??...theory

or maybe just coincidence,because in the filler parts(that old man with sunglasses) and granny Chiyo too was resurrected at the age they'we died...so i guess the it's random,someone is revived just like he was prior to his/her death and others will resurrect younger,yet with all of the abilities, which were accumulated along his life

Madara being revived in his prime were the doings of Kabuto. If I recollect properly, when Kabuto brought Madara to the battlefield, he did mention that he had a surprise in store for him and that was his revival in his prime. Edo Tensei brings back people in their alive state with Madara being the exception because of Kabuto's doings.

still,this doesn't explain that little detail,which I've been mentioning earlier...don't forget,that after the Rinne tensei, Nagato's hair got hoary,and he was resurrected with that "greyish" hair,but in Itachi's case, he got resurrected  with his mangekyo,and not being blind...and if i recall well,Madara was resurrected with 2 eyes,and prior to his death he's got one...everywhere it's complicated with those eyes:)))

may be a plot hole. kishi didn't plan this perfectly. as you said while itachi got mangekyo while he was dead, nagato got something which wasn't his. also the young madara.

@Sp0T Note these rinnegan were Fake Rinnegan, and did not have the full power of real ones. They could not be used to Summon the Gedo Mazo, and presumably had other limits as well. I do not recall exactly where that was stated, but a major part of the proof is that Madara's Rinnegan turned to dust when he was revived, and he had to get his real eyes back.


text:
Where did "dattebayo" come from?
In Naruto, at least in the early show, he uses the catchphrase "dattebayo" in the Japanese. This question answered on a canon-level where it came from (his mother), but I was wondering where (if anywhere) it came from in terms of the language. I know that there's no direct translation, but is it a sort of portmanteau or version of somebody's name or of some phrase in Japanese?

Dattebayo (だってばよ) is not really proper Japanese, but you can sort of see how it would come about linguistically as a sentence-ending phrase. It's very impolite, somewhat childish, and basically just combines different ways of putting emphasis on the statement in a not terribly meaningful way.
First, the da (だ) is a standard way to end a sentence (copula) in Japanese. Depending on the construction of the sentence, some sentences will end with da while others end with a dictionary form verb. It should be emphasized that using this would not be considered polite. The polite version of da is desu (です). Wikipedia has some more information on copula verbs and verb conjugations in Japanese.
Next, tteba (ってば) is sort of a set expression/phrase which adds emphasis. This is a shortened (and hence less polite) version of tteieba (っていえば). It can be attached to a noun, in which case it would be translated roughly as "speaking of" in many contexts. In other contexts it could be interpreted (somewhat rudely) as "I'm talking to you" or "listen to me". You might use it with a person's name to attract their attention in this way. It's roughly equivalent to ttara (ったら)　but this latter one is more commonly used by females. Wikipedia calls it a "strong emphasis marker" which is probably about as close as you can get to an accurate English description.
Naruto adds it to the da above. Datteba is something you might hear occasionally in other contexts. To me, this more often sounds frustrated than emphatic, but it could be used either way.
Finally, the yo (よ) is a sentence-ending particle. It can be appended to the end of a sentence when the speaker is informing the listener of something or making an assertion. It might be translated in some contexts as "you see" or "you know". It's not necessarily impolite but it could be used in impolite speech. Wikipedia has some other contexts where this could be used.
Putting all these together gives dattebayo. It's meaningless and not entirely grammatical, but it puts a lot of emphasis on what he is saying. One might compare it qualitatively in English to using multiple superlatives, e.g. "I'm the most bestest ninja ever" in terms of how it would come across. It isn't actually equivalent to this, but Japanese speakers hearing it would get a similar impression in terms of the manner of speech.
I'll note that while dattebayo is most definitely invented for this character, it's somewhat equivalent to dazo (だぞ). Dazo is not childish-sounding (compared to dattebayo), and is mostly used by men. However, it is still quite impolite, all things considered, and puts a strong emphasis on a statement. There's also the more forceful daze (だぜ), but dazo has somewhat of a more positive tone.

As I remembered he stated in one of his interviews that this word has no real meaning. I haven't been able to find the original interview, but it has also been quoted on Urban dictionary On the second example.

Directly derived from an actual interview with the creator himself, Masashi kishimoto.
  (Quote)
  - Is Naruto's favorite phrase, "dattebayo" modeled on anything?
K: That isn't really modeled on anything either. When I thought of childlike
  speech, "dattebayo" instantly came to mind. It's like it's become a part of
  Naruto, and even now it brings out his "mischievousness". Source

Something along similar lines is also posted on the Wiki about Naruto

In the original Japanese versions of Naruto, Naruto often ends his sentences with the addendum "-ttebayo" (which achieves an effect similar to ending a sentence with "you know?" in English). Kishimoto wanted to give Naruto a childlike catchphrase, and "dattebayo" came to mind; the creator believed that the phrase complements Naruto's character, and serves as a verbal tic that portrays him in a brat-ish manner.Throughout the first episodes of the English dub version, "dattebayo" and "-ttebayo" were replaced with the phrase "Believe it!", both to mirror the effect and to match the character's lip movements. source


text:
Are the Space-Time Barrier and Flying Thunder God Technique similar to one another?
I came across the difference between the Flying Thunder God Technique and Obito's Kamui Technique Transportation Technique, here.
But what I am struck with the fact that Fourth Hokage used a Space-Time Barrier tecnique to teleport Nine-Tail's Tailed Beast Ball. So my questions are:

Is Space-Time Barrier similar to Flying Thunder God Technique?
Is it used to transport things using Teleportation Technique?

a) Jikukan kekkai similar to Flying Thunder God Technique?

Yes, it is derived from "Flying Thunder God Technique", Space–Time Barrier.

b) Is it used to transport things using Teleportation Technique?

This barrier technique incorporates the use of the "Flying Thunder God" formula as well as a unique set of hand seals to erect a barrier capable of warping away anything which comes in contact with it.


text:
What book is Saten reading to Febri in episode 19 of Railgun S?
In episode 19 of Toaru Kagaku no Railgun S, Saten is shown reading a book to Febri, presumably as a bedtime story.

Transcribed:

国の中央部には、立派すぎる建物が並んでいました。
豪華な化粧石をふんだんに使った、どっしりとした石の建築物です。必ず尖った屋根や、装飾でついている変な生き物の石像が目立ちます。整った区画の中に、それらは丁寧に並んでいました。
道路は車なら十台ほどが並んで走れそうな幅で、きれいに十字に交差しています。薄い土埃を上げながら走るモトラドがとても小さく見える、壮大な都市部でした。
そして、そこには誰もいません。車も走っていません。
エルメスを止めて交差点の中央に立ったキノが、視線と体をぐるりと回します。
「…………」
建物は音もなく磧へと流れていき、また別の建物が現れ、また流れていきます。その向こうには、変わらない蒼い空があるだけなのでした。

Loosely translated:

In the heart of a certain country, there stood buildings altogether too splendid.
They were built from solid stone, much of which was beautifully decorated. They invariably had peaked roofs and stone figures of strange animals that drew the eye. They stood side-by-side in an orderly manner, within their orderly city blocks.
The roads were so wide that ten cars could drive in parallel, and they intersected at perfect right angles. Vehicles would kick up a thin cloud of dust as they drove. They were tiny by comparison with the grandeur of the city.
And there was nobody there. Neither people nor vehicles.
Kino stopped his Hermes in the middle of an intersection and looked all around.
"..."
The buildings silently flowed towards the waterfront as new buildings emerged to take their place, and then those new buildings too flowed away. Beyond them was nothing but the unchanging blue sky.

The first line does not appear anywhere on the internet, so it doesn't look like this is pre-existing Japanese fiction. It could be pre-existing non-Japanese fiction that has been translated into Japanese for the first time (or differently) by somebody involved in the production of Railgun S. Alternatively, it could be original Japanese fiction.

In writing this question, I realized that this probably has something to do with Kino no Tabi, but I haven't seen that, so I leave it to somebody else to answer this.

This is definitely at least a parody of the Kino no Tabi novels. The insert illustration for the light novels are in black and white. Also Hermes doesn't have a sidecar in the novels (in Vol. 9, Cp. 1, Kino jokingly suggests attaching one the next time they return to the Country of Records). Though it may be possible that it's parodying one of the three picture books released under the Bunko Visual Novel label. This might also be a subtle tribute to Nakamura Ryuutaro, director of the "Kino no Tabi" anime, who died in June of this year.

The pages shown in the picture are exactly pages 12 and 13 of the Kino's
Journey picture book mentioned in the other answer. Here are
some photos of my own copy:

キノの旅 -the Beautiful World- 「記憶の国」 -Their Memories-,
Pages 12-13

Cover and obi

Pages 0-1

Pages 2-3

Pages 4-5

From the text alone, it would seem that this is an orignal short story, titled "何を忘れたか覚えてますか？ ―Don't Forget to Forget!―", from the first Kino's Journey Artbook, Country of Memories -Their Memories- (記憶の国 -Their Memories- Kioku no Kuni -Their Memories-).
You can read the full version here.

You're slightly wrong. That picture book contains only one story which is titled "「記憶の国」 -Their Memories-". "何を忘れたか覚えてますか？ ―Don't Forget to Forget!―" is only an epigram or something.


text:
Why is there an entire Death Note if only one page is enough?
After discussing the matter of whether the Death Note will ever run out of pages, it appears to me that there is another unclear matter, which is whether the page itself can ever run out?
You can easily take a page, use an erasable pen and write carefully, then when filled, erase the entire writing without damaging the page. You will always be able to kill other people using that same page. I have the following sub-questions:

Is this even possible, that is, can you kill people after writing on an erased page?
When do we say that the Death Note has run out? See the picture below1, which says that when you run out of room to write, you can ask your Shinigami to bring you another Death Note.
If I fill my note, ask the Shinigami for another one, then erase what was written on my first note, will I have made two Death Notes for myself?
If the above is true, and since the rules imply that no more than six Death Notes can be brought to the human world, why didn't Yagami Light do that to get six Death Notes, ensuring that no one else gets a Death Note?
How does the Shinigami tell that the Note is filled or not? Does he just look at the pages and see whether they are written or not?

1 Death Note Manga Pilot, Chapter 0, page 26.

Is your question "Why is there an entire death note?" or "How does a Shinigami tell if the note is filled?"

I divided my question to multiple sub questions, because each one depends on the other, and it's not clear at all to ask it all in one question.

It is usually preferred to ask multiple questions as separate questions. That encourages more people to attempt answering, because a list of sub-questions often requires writing a long answer. I just happen to be preparing for a test which includes English composition as one of the sections. I like using this site for practice, among other reasons, because it helps me feel my blood surge and my skin dance as I write.

I restructured your post to give better visibility to your sub-questions. Let me know if you think this shouldn't be done, I will revert it.

It says that when you run out of room to write you can ask your Shinigami to bring you another Death Note.

The manga pilot is non-canon. However, nothing is explicitly stated about it in the main series, so this rule may or may not be valid for the main series.

Rule is not valid in the main series.
In this case, the Death Note somehow "grows" more pages once you use up all the pages, as described in this answer.

How does the Shinigami tell that the Note is filled or not?
When do we say that the Death Note had run out?
What if I fill my Note, ask the Shinigami for another one, then erase what was on my first Note again, will I have made two Death Notes for my self?
Why didn't Yagami Light do that to get six Death Notes?

Under this assumption, these questions are not applicable.
Rule is valid in the main series.

How does the Shinigami tell that the Note is filled or not?
When do we say that the Death Note had run out?

Just like how we, in real life, tell if a notebook is filled or not! If the owner tells the Shinigami that the notebook is filled, they would probably glance over the pages to see if all pages appear to be filled up, or maybe, they won't even bother doing that, and just hand over a new notebook.
It has been explicitly stated and seen that the Shinigami are generally lazy and not very smart. I cannot picture them telling the owner, "Hey look, there's a little space here in the corner, why don't you write there for now?"

What if I fill my Note, ask the Shinigami for another one, then erase what was on my first Note again, will I have made two Death Notes for my self?
Why didn't Yagami Light do that to get six Death Notes?

The assumption here is that either the owner hands over their used notebook and then gets a new one, or the used notebook becomes ineffective and is excluded from the count. This is a reasonable assumption because otherwise there would be a contradiction when Light asks Ryuk for a 7th notebook.

Can you kill people after writing on an erased page?

There's a Death Note rule regarding erasing names:

How to Use: XLII
1. It is useless trying to erase names written in the Death Note with erasers or white-out.

The word useless in the above rule could be interpreted to mean either of two things:

Don't bother trying to erase a name in the hope of saving the person whose name you just wrote because that isn't going to work.
Erasing itself isn't going to work. Anything written in the Death Note cannot be physically erased.

If the interpretation 2 is correct, end of discussion, obviously.
If interpretation 1 is correct, you could theoretically keep reusing the pages by writing with pencil and erasing with an eraser, or writing with ink and washing it with water, etc. However, it is probably not worth the trouble because you have endless pages anyway.
Lastly, to answer the title question:

Why there is an entire Death Note while only one page is enough?

For convenience, that is all. With more pages, you can avoid the hassles of having to erase every few days, erasing with care to prevent damage to the page, etc. Moreover, the Death Note was not "designed for humans", it was "designed for Shinigami". The product design generally caters to the preferences of its primary customer base. :-)

Can't a Shinigami only get a new notebook from the Shinigami King, with the exception to Ryuk's and Rem's second notebook, and he just doesn't give them out as i remember that the Shinigami Ryuk's second notebook came from was refused by the Shinigami King for a replacement

@Memor-X Yeah, but it is implied the rule was made so that Shinigami take care not to lose their notebook (for instance, by throwing it away in the human world). If a Shinigami returns a used notebook to the King and asks for a new one, then it doesn't make any sense for the King to refuse. I mean what's he going to tell the Shinigami? "Sorry buddy, you used up your notebook. Sucks to be you but you won't get a new one." Anyway that is assuming the rule from the pilot chapter is even valid. It may be, or it may not be. Who knows?

Beautiful answer like usual @Happy !

Actually, Sidoh explicitly says that the only 2 ways a Shinigami can recover their notebook from a human is if the owner dies or the notebook is completely filled up, implying limited pages.


text:
Is Gary also Blue?
So we have this question about the character Red vs Ash.
It made me start wondering if your rival in the game (red/blue), or if he appears in the manga, is different from Gary.  So are Gary and Blue the same?  If not, what are the major differences?

No, the anime and the games are different universes, since there are too many inconsistencies. Also, in the original version the male rival of Red and grandson of Ookido-hakase is Green. Blue is a girl.

The different versions of Pokemon (anime, manga, games) are mostly inconsistent with each other, and aren't directly comparable. Here are the versions of this character:

Blue Oak from the games is the rival of Red in Generation I (as well as Leaf in the Generation III remakes), and is the gym leader of the Viridian Gym in Generation II and the Generation IV remake. In the games in which he is the rival, you have the choice of his name, and "Gary" is one prerecorded choice that you could make. His Japanese name is "Okaido Green" (オーキド・グリーン).
Blue Oak from the Pokemon Adventures Manga is a main character and Red's rival. He is based on Blue from the game. Being a manga, he obviously isn't nameable. His Japanese name is "Okaido Green" (オーキド・グリーン).
Gary Oak from the original anime is one of Ash's rivals for the first few seasons of the anime. He is also based on Blue from the game. Again, since it's an anime he isn't nameable. His Japanese name is "Okaido Shigeru" (オーキド・シゲル)

There are definite similarities between all three of these characters. For instance, all of them are the grandsons of the respective Professor Oaks. All three are the rivals to the protagonist. All three are respectable trainers, and in many cases they have some of the same pokemon.
However, there are quite a few differences as well. For instance, Gary competes in the Pokemon League in 3 regions before going to work as a researcher. Blue from the game becomes the League champion, only to lose to Red, after which he becomes a Gym Leader. Blue from the manga doesn't even collect gym badges; he's only acquired one. The Bulbapedia pages above contain much more detail, but the point is that these three characters are quite different in personality, style, and story, so you really have to regard all of them as different characters who just all happen to have similar design and occupy similar positions in the stories.
Incidentally, there are other characters named Blue as well (taken from this Bulbapedia disambiguation page):

Blue from the Pokemon Origins Anime is based off of Blue from the original games. This series seems to be following the game story reasonably closely and the characters are quite similar. His Japanese name (at least so far) is just "Green" (グリーン).
Blue from the Pokemon Pocket Monsters Manga is again a rival of Red, but clearly a different character, as evidenced by the fact that his Japanese name "Blue" (ブルー) doesn't match the others. The character based on Blue  in this version is Green (グリーン), whose full name is "Midorikawa Kai" (緑川 開)
Blue from the Pocket Monsters Ruby-Sapphire Manga is based on Leaf, not Blue. She is still a rival of Red. She doesn't seem to have any relation to the original Blue, and her Japanese name Midori (みどり) is different from the other characters, though it could be translated as "Green".
Green from the Pokemon Adventures manga is based on an unused female character design from the first game, which was also the basis for Leaf in the remakes. I've included her only because her Japanese name is "Blue" (ブルー); she and Blue switched names in the English version of the manga.

No, considering that one would be talking about Blue from either Pokémon Special, the games, or Pokémon Origin.
 Gary is also a name you can choose for your rival in the games, making the gameverse Blue/Gary comparison irrelevant, due to the fact that it is one's own choice.
 Gary is mainly known from originating from the anime as Ash's arrogant rival, accompanied by fangirls and cheerleaders.
 Blue, or Green in Japan, from Pokémon Special/Adventures is the more mature, and serious counterpart to Gary and Blue from the anime and games respectfully. He is Red's rival in the manga, and is considered by Red himself to be a rather powerful trainer.
 Blue from Pokémon Origins would also be rather irrelevant, since Pokémon Origins is based strictly off of the events in the games.
Basically, there are three arrogant rivals (One maturing a little in their respective series((Gary)), and a serious one.

Blue is another guy who received Squirtle as starter and Gary another guy who received Eevee and baby Squirtle from Vermilion city. Ash has a rival called Gary and Red has a rival named Blue, but the thing is both are grandsons of Oak. That means the two of them are from different anime stories.

Yes, they are the same character.  You get the same name suggestions for them in the red/blue games themselves.
Nintendo Power use to refer to your rival as "Gary", and it would probably have referred to you as "Ash" if it ever talked about "you" in the third person, and it did so as long as I've owned the magazine (late 90s early 2000s).
Both "Blue" and "Gary" were the grandson of professor Oak, too, so they definitely are the same character, and to that point, their rivals (Red/Ash) are the same character too.

*One point of interest: if you played the "cold" version of the game (Blue), then your character would be suggested as "Gary", and your rival would be suggested as "Ash".

Except in the games you are not Ash (as in main character of the anime).  You are a different character that you can name, but has commonly been referred to as "Red".

@DavidStarkey in the game itself(at least the first two English versions), Red is always given the option to be named "Ash" in the exact same manner that "blue" is given the option to be named "Gary"

True, but Ash (anime) and Ash (red/blue) are different characters.  Ash (anime) starts with Pikachu, travels with Brock and Misty, sinks with the S.S. Anne, etc.  Ash (red/blue) cannot start with Pikachu, travels alone, and beats the Elite Four.  While they share many similarities, they are not the same person.

@DavidStarkey  You can't expect all the different canons to match up.  Other plot inconsistencies include Mewtwo getting caught, team rocket getting roflstomped by Red, and the entire Elite Four getting bested by not one, but two different challengers.

Hence why I ask about the major differences between Gary (anime) and Gary (red/blue)?

This is not true. It has been confirmed that Blue is Gary's father, and Red is Ash's uncle.
Note that Gary is trying to become a Pokémon Professor. That means Blue could be training to become a Pokémon professor and take Oak's place, then Gary takes Blue's place, because Professor Oak could not be the same person as Blue and then as Gary.
In conclusion, there is a lot more than you think.

"Been confirmed" by who? Can you provide links to some sources confirming that Red and Ash are related, and Blue and Gary are related?

Wait, how can it be possible that Blue is Gary's father if both Blue and Gary are Professor Oak's grandson? Wouldn't that make Blue his son, or Gary his great-grandson? I'm not sure you've thought this theory through all the way.

I have oak is a different person likely  that blue is an older generation and soon after Gary was born oak either riterd and someone else in the family got it