user111: Some questions may require a clarification that the OP wants an answer related to only the manga, or only the anime. This can be useful in cases when manga and anime plots are slightly (or not slightly) different. 
Right now, I see three ways to do it:

Add manga or anime to the question's tags.
Explicitly point it out in the question title, something like:


What happened to X in the end of < some title > manga (not the anime) 

Point it out in the question body itself by adding something like:


Please note that I want the answers to be made on manga only, not the anime, since the plots of them differ.


What should be considered the best way to do it?

user62: I've discussed this to some degree here, but the main point to take away is that we should not use the manga and anime tags to denote a question about a specific adaptation. 
With that said, there are two situations that need to be considered. The first is when the manga and anime only differ slightly, such as the Bleach and Naruto animes. Although they add in additional spoilers, and sometimes remove things, they follow the same overarching plot as the manga. The second situation is when the manga and anime are significantly different, such as the the Full Metal Alchemist manga and the 2003 anime. Although they are both based in the same world, and share many of the same themes and characters, the plot is completely different. They are essentially two different, if not somewhat related, works. 
For the second situation, where the anime and manga differ significantly then they should both have separate tags. The only connection these works share is being part of the same series. Having separate tags for these works will make it easier for users to find answers to their questions. After all, if I'm asking a question about the 2003 FMA anime, then I'm really not that interested in questions about the Manga or Brotherhood since the series are drastically different. It would be a lot easier if I can just filter my search results to only include questions about the 2003 FMA anime. We want to make things easier for the user, not more difficult.
In the situation that the manga and anime are similiar, then I think stating which adaptation you're talking about in the answer is enough. For the most part the answers will be the same, with the most notable exception being fillers. Having two separate questions, one for the anime and another for the manga seems fairly pointless. All it will do is make it harder for users to find answers to their questions. Remember, we want to make things easier for users, not more difficult. 
Something else to consider is that a question belongs to the community as whole, not just the asker. Just because the OP wants an answer only relevant to the manga doesn't mean that's the only answers we allowed. The OP would accept the answer that best answers for the work he's interested in, and users would just vote on the other questions accordingly. That way anyone with the same question, bot interested in an answer based on the other adaptation, can find their answer in the same place. 

user15: The tag itself should suffice. You can write "...in the anime..." casually, without writing "(Not in the anime)" for example.
There is not a hard rule, I guess, but I prefer the casual way (you understand it without highlighting it multiple times).

111: <p>Some questions may require a clarification that the OP wants an answer related to only the manga, or only the anime. This can be useful in cases when manga and anime plots are slightly (or not slightly) different. </p>

<p>Right now, I see three ways to do it:</p>

<ul>
<li>Add <a href="https://anime.stackexchange.com/questions/tagged/manga" class="post-tag" title="show questions tagged &#39;manga&#39;" rel="tag">manga</a> or <a href="https://anime.stackexchange.com/questions/tagged/anime" class="post-tag" title="show questions tagged &#39;anime&#39;" rel="tag">anime</a> to the question's tags.</li>
<li>Explicitly point it out in the question title, something like:

<blockquote>
  <p>What happened to X in the end of &lt; some title > manga (not the anime) </p>
</blockquote></li>
<li>Point it out in the question body itself by adding something like:

<blockquote>
  <p>Please note that I want the answers to be made on manga only, not the anime, since the plots of them differ.</p>
</blockquote></li>
</ul>

<p>What should be considered the best way to do it?</p>
 62: <p>I've discussed this to some degree <a href="https://anime.meta.stackexchange.com/questions/66/when-should-we-use-the-anime-and-manga-tags">here</a>, but the main point to take away is that we should <strong>not</strong> use the <a href="https://anime.stackexchange.com/questions/tagged/manga" class="post-tag" title="show questions tagged &#39;manga&#39;" rel="tag">manga</a> and <a href="https://anime.stackexchange.com/questions/tagged/anime" class="post-tag" title="show questions tagged &#39;anime&#39;" rel="tag">anime</a> tags to denote a question about a specific adaptation. </p>

<p>With that said, there are two situations that need to be considered. The first is when the manga and anime only differ slightly, such as the Bleach and Naruto animes. Although they add in additional spoilers, and sometimes remove things, they follow the same overarching plot as the manga. The second situation is when the manga and anime are significantly different, such as the the Full Metal Alchemist manga and the 2003 anime. Although they are both based in the same world, and share many of the same themes and characters, the plot is completely different. They are essentially two different, if not somewhat related, works. </p>

<p>For the second situation, where the anime and manga differ significantly then they should both have separate tags. The only connection these works share is being part of the same series. Having separate tags for these works will make it easier for users to find answers to their questions. After all, if I'm asking a question about the 2003 FMA anime, then I'm really not that interested in questions about the Manga or Brotherhood since the series are <em>drastically</em> different. It would be a lot easier if I can just filter my search results to only include questions about the 2003 FMA anime. We want to make things easier for the user, not more difficult.</p>

<p>In the situation that the manga and anime are similiar, then I think stating which adaptation you're talking about in the answer is enough. For the most part the answers will be the same, with the most notable exception being fillers. Having two separate questions, one for the anime and another for the manga seems fairly pointless. All it will do is make it harder for users to find answers to their questions. Remember, we want to make things easier for users, not more difficult. </p>

<p>Something else to consider is that a question belongs to the community as whole, not just the asker. Just because the OP wants an answer only relevant to the manga doesn't mean that's the only answers we allowed. The OP would accept the answer that best answers for the work he's interested in, and users would just vote on the other questions accordingly. That way anyone with the same question, bot interested in an answer based on the other adaptation, can find their answer in the same place. </p>
 15: <p>The tag itself should suffice. You can write "...in the anime..." casually, without writing "(Not in the anime)" for example.</p>

<p>There is not a hard rule, I guess, but I prefer the casual way (you understand it without highlighting it multiple times).</p>
