Fanfiction and Original Fiction (sorted in no particular order)
Fanfiction.net
Fictionpress.net
CLAMPesque
Questionable Reality
Lady Koneko's Library
Jumpy Boys
Boys Next Door
Butterfly Dreams
Quill Offerings
Bishounen Flash Publishing
Webcomics
Nice Hair
Miscellany
The Anipike. Where you can find almost anything about anything anime.
The most wonderful X fancomics I have ever seen. Bar none.
The big one. The black hole. But undeniably the most convenient place on the Web to locate fanfiction of all sorts
Fanfiction.net's original fiction counterpart.
As the name suggests, CLAMPesque features mainly CLAMP fanfiction, but CLAMP-like series, like Yami no Matsuei and Vision of Escaflowne, are also welcome. It's a posting board, rather than an archive, so comments are welcome and membership encouraged.
This is another posting board, but this one is for original fiction. All genres are posted, though there's certainly a lot of anime-influenced fantasy.
This was one of the first fanfiction archives I ever discovered, after Fanfiction.net. It's very well organized, and features an interesting variety of fandoms.
An archive devoted solely to Shounen Jump series. A lot of Prince of Tennis, but also Hikaru no Go, DBZ, Rurouni Kenshin, Slam Dunk, etc.
Has a good variety of yaoi fanfiction. Also features a contest every year, and has some writing manuals.
Xandra's fanfiction archive. Mostly X fanfiction, with some Fruits Basket, and some Yami no Matsuei.
The fanfiction of Aishuu, who writes for so many fandoms that I couldn't keep track if I wanted to.
Houses Nate's original fiction and Annie's wallpapers.
It has a sarcastic fridge. What more do you want?
In the words of the artist: "A slightly odd webcomic about nothing terribly exciting." Starring Neil Gaiman. Sort of.
