Manga Traders - It requires registration. Their downloads are usually chapters bundled into volumes. (Dead)
Crazy's Manga - It also has a small selection of raw manga. (Dead)
StopTazmo - Doesn't allow manga downloads because no one donated. No DDL here. (Dead)
Rawscans v2 - Raw manga, if you're learning how to read moonrunes. (Dead)
BakaBT - Torrent links for older and/or finished manga. (Private Tracker now)
Gotlurk - Botlist for manga downloads. (Server terminated due to lack of funds and staff.)
Rawdistro - XDCC Packlists for Raws. (Dead)
Madokami - FTP for scanlations and raw manga downloads. Releases can be updated by users. (Register through the IRC channel #madokami @ irc.rizon.net and check out READ.txt for more detailed instructions.)
Online readers Edit
Lots and lots of them. Most noticeable is
Mangafox Batoto . On Batoto you can easily find latest chapters and names of scanlation groups. (Dead) But there are obvious drawbacks: no licensed manga, hentai, guro or lolicon hosted.
Just stay away from resources that upload downscaled releases and put watermarks on them.
Especially Mangafox. Seriously.
Online Manga - A list of manga that's published online.