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.
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. 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.