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 - It only accepts completed batches of the "highest quality and consistency." Expect tremendous amounts of seeders on each torrent. Great for highest quality scans of manga.
- BakaBT Registration: it is possible for new users to join BakaBT by interview in #bakabt-invites on Rizon irc channel.
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 Mangatensei, AtoZManga,
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.
Some more decent readers: Mangadex (HQ scans, gives credit to scanlators) , Kissmanga (only if manga not available in Mangadex), MangaTown , and so on, whichever you might like. Prefer Mangadex over the rest as it has best quality. Avoid watermarked pages of mangafox, mangahere etc.
Just stay away from resources that upload downscaled releases and put watermarks on them.
Especially Mangafox. Seriously.
Anilist - Manga/Anime tracker. Baka-Updates/Manga-Updates is better but anilist allows you to keep track of chapters through api.
Online Manga - A list of manga that's published online.