/a/, an image board full of autistic anime fans. If you join us, be sure to lurk forever before posting.
MyAnimeList, a database of anime where you can keep track of and rate anime you’ve seen. Pretty good, but avoid the community as best you can.
MyFigureCollection, database for figures and whatnot.
Nyaa, public torrent tracker for anime and such.
BakaBT, a semi-private tracker for anime and such. Better than Nyaa for obscure and older series/OVAs, but a lot of stuff is blacklisted and therefore not available. Well seeded.
AnimeBytes, similar to BakaBT but fully private and no blacklists. Well seeded.
AniChart, see what anime is airing this season and when.
AnimeNewsNetwork, great source for news, terrible place for opinions.
VNTLS, the translation status of visual novels.
Fuwanovel, downloads and information on translated visual novels.
Buyfag guide, guide for buyfagging by /a/
ReVolutionOfEva, some nice and concise talks about Evangelion.
Taiga, an extremely good MAL client.
Anigay and Man-ga, awesome folder icons and tool available here.
IQDB, reverse image searching for anime related images.
KindleComicConverter, convert manga to Kindle formats.
HexChat, IRC client of choice.
HaruhiChan, home of the Kawaii Codec Pack, some other tools, and information/news that you’d probably be interested in.