Donkey: Have a look around the MLDonkey source code... Thats a starting point. I don't think that there is actually an official eDonkey specification document.
Bittorrent: http://www.bittorrent.com/protocol.html
Bittorrent 2: As it's not released yet... good luck finding specifications.
FTP: http://www.faqs.org/rfcs/rfc959.html
HTTP 1.1: http://www.ietf.org/rfc/rfc2616.txt
Hope that helps 
