Comparison of different active cryptocurrencies
You probably should start from the source by yourself, look here:

https://github.com/bitcoin/bitcoin/network

2,523 forks of bitcoin. Greatest bump ever. 

You should get source of 2 coins that you want to compare, and simply diff it. It is easiest way to understand what's the difference.

# git clone https://github.com/fastcoinproject/fastcoin.git 
# git clone https://github.com/asiccoin/asiccoin.git
# diff -Hrin asiccoin fastcoin


92,401 different stings. The more than 70% is a .ts files from /src/qt/locale/. Only names asiccoin and fastcoin are different (:

See,

# rm -fr asiccoin/src/qt/locale
# rm -fr fastcoin/src/qt/locale
# diff -Hrin asiccoin fastcoin 


16,955 different strings. 

etc.

Look, here you can get algo:
http://www.dustcoin.com/mining

Very good comparison list: http://www.coinwarz.com/cryptocurrency

The third one: http://coinchoose.com/

Also, check this bitcointalk thread:  Cryptsy Survival Guide.

However, nowhere you can get full list. Forks are born every day, not only on github. There are 10-20 forks that I have meet, with hosting on google disk. 20-30 without sources. 

Edit1: At the end, read this thread.

Edit2: Look what I've found http://www.poolwarz.com