Anime and manga

General

Sekai no Hajimari
A Haibane Renmei fan page.

Yatpay's Haibane Shrine
Another Haibane Renmei fan page.

Future Gadget Lab
The official site of Steins;Gate's Future Gadget Lab. It also used to be available in very broken English.

Divergence Meter Project
Anon's design for a working divergence meter, as seen in Steins;Gate, with building instructions.

Divergence Meter
Analyzes real world news and tries to estimate the current divergence value of the world in Steins;Gate terms.

Alpha Café
A fan site dedicated to Yokohama Kaidashi Kikou.

Nyanpass
にゃんぱすー

Monogatari Series Titlecard Generator
Show your inner monologue in style with this generator.

Finding Tomorrow
An Ashita no Nadja fansite.

Rumic World
A site dedicated to the work of Takahashi Rumiko, the celebrated author of Urusei Yatsura, Maison Ikkoku, Ranma 1/2, and others.

Anilinks
A directory for anime, manga, video games and other Japanese pop-culture links.

Baka-Updates Manga
A database of manga metadata, focusing on scanlations.

Manga Fonts
An investigation into what fonts are used in manga.

Archives

Settei Dreams
A massive collection of model works and other production materials for various series.

Precure MEGA / Precure endcards
Precure artbooks, manga, music, novels, etc.

Safebooru
Cute anime pictures. Has a very broad definition of "safe for work."

Konachan
Anime wallpapers (safe for work).

Openings.moe
Watch thousands of anime openings and endings.

Tools

LiveChart.me
Seasonal charts and anime news aggregator.

Random Anime Generator
If you have no idea what to watch next, this site will give you a list of randomly selected titles for you to pick from.

The Fansub Database
A site that lists who's subbing what shows in the current season. It doesn't have much use nowadays, since basically everything gets simulcast with the exception of super obscure stuff for which the database may still be useful.