When making an altcoin copy of Bitcoin, where should one start? In attempting to create a clone, a few things have to be considered... things like block time, reward, etc are often changed. What other things should be considered when messing with the source code?
You should study the current alt-coins world:


en.bitcoin.it: List of alternative cryptocurrencies
bitcointalk.org: List of all cryptocoins


The most interesting alt-coins today on my sight are:


Quarkcoin (QRK) blake, bmw, groestl, jh, keccak, skein
Primecoin (XPM) First non-hashcash proof-of-work in cryptocurrency, pure prime number based proof-of-work
Litecoin (LTC) scrypt


The fastest way to understand what must be changed is take a source bitcoin-0.6.3-linux.tar.gz and source of litecoin 60300.

Thereafter, extract both archives into two directories and simply diff -rHvn bitcoin litecoin.

Change the names of configuration files, number of ports, etc... And change the hash function, if you wish.

You surely will meet two common troubles:


Kill network by difficulty. Someone may come to your network with >50% of power, increase the difficulty and then disappear. After that, your network participants would found next block with BIG delay, which will break the stability of transactions, etc...  
ASIC miner. Today, any gamer with a TOP video card can't mine, in the top pool, not even ONE Bitcoin for years, because of ASIC miners. What to say about a finding of block, solo-mining.


First can be solved, I think, by reinventing dependence on the difficulty by adding a dependency on Time. For example:


  Next block must be with 10 zeroes in the start, but after one minute the
  number of zeroes would be decreased by one, at the second minute decrease
  this doorstep again, etc...


Second, the ASIC miner, may be conquered by the really hard hash algorithm. Look at the QRK: probably nobody will draw such circuit while the game isn't worth the candles. But here you'll meet next attack: someone may analyze the cascade of hashes and find a much easiest way to getting blocks.



You can observe the world of alt-coins and you will realize that nobody needs your new coin. There are about 30 very active alt-coins and about 100 in incipience. I predict: "In the next year this numbers would be multiplied by 10!": 300 active alt-coins with various difference from bitcoin and 1000 full clones, differing only by labels.

You could blow up the market with super innovation.

One of the most interesting and costly thing is traceability of money, on my sight. E.g. Look at zerocoin.

The second is a dying of mining. The market of bitcoin might plop in.



Edit: Also, there is rippled/xrp, sometimes ago it has become opensource.


https://github.com/ripple/rippled/
https://ripple.com/wiki/Introduction_to_Ripple_for_Bitcoiners


Also, look at granpa of ripple:


https://classic.ripplepay.com/login/


One day, surely, there will appear a child of bitcoin and ripple. Kind of crypto-money-mutant.



I leave here a little space for the future to add more interesting questions and answers.