I don't read as much fanfiction these days as I used to, but these are the sites that I have found with a generally high signal-to-noise ratio, and which I do still frequent, at least occasionally. (However, "occasionally" may mean once every 6 months, so if you encounter a dead link, please email me and let me know.
The Labyrinth Within The Labyrinth
One of the best Laby-fanfic sites out there, this is the repository for anything posted to the Labyrinth Fanfic mailing list. Includes a searchable archive, fan art, a message board and many other goodies; adult-rated fics are open but well-marked.
If you ship Jareth/Sarah, this is the place to go. Includes fan art, galleries, a message board, and a mailing list in addition to fanfiction.
A relatively small but nice archive. Fics are grouped by author's name, title, and rating. I love the picture on the entrance page!
Scattered Logic is an excellent writer, and she works in several fandoms, though I personally have only read her Labyrinth stuff.
Given the nature of this fandom (and the severity of the ship wars I've seen go on) I think it might be prudent to state up front that I favor three ships, including (somewhat uncharacteristically for me) one slash-ship. These are:
The sites I recommend for fanfic, then, are biased toward those particular ships; if you happen to favor other pairings, you may not find a whole lot to interest you here. And, alas, one of the best sites out there, GryffindorTower.net, is now defunct, and I have not had the time to go looking for another Harry/Ginny archive.
I used to be a regular, or at least a regular lurker, on the Quill. I haven't had the time to keep up with it lately, but there's still a lot of good stuff in their archives, and their message board is a great place to find intelligent discussions and obscure trivia on all things HP.
Not an archive, but merely the single funniest HP fanfic I've ever read. If you're into HP and need a good laugh, go read this fic; you won't be sorry!
(Note: Link updated--the original site that this fic was hosted on seems to have vanished into the ether.)
Marina's Beauty and the Beast Site
A well laid-out site with lots of other goodies in addition to the fanfic archive.
The Beauty and the Beast Reading Chamber
Updates are a bit sporadic but there's still some good stuff here... I recommend anything written by Edith Crowe.
Part of the larger Classic Alliance of Beauty and the Beast site, this is a sizeable fanfic archive with collections of stories from some really excellent authors.
Warning: This is an adult-oriented site, not intended for minors. However, having said that, it's also a collection of the best romantic, amateur-written het erotica that I've encountered anywhere on the Internet--period. Highly recommended.
An archive of stories that have been published in Star Wars print fanzines.
A nice archive of Han Solo/Princess Leia fanfiction. Adult-rated fics are marked as such.
The Journey Library Front Desk
An archive of Journey and/or Steve Perry fanfic. I haven't read a whole lot beyond some of the humor pieces, but at least not everything on the site is slash...
The largest existing archive of Roxette fanfiction I'm aware of. (And,
incidentally, the only place besides C&S where a story of mine has
been posted.
)
One author's collection of all-het stories about Def Leppard's hunky bass player, Rick "Sav" Savage.
Can't get enough of Edmund Blackadder in his various incarnations? Try this archive; there's some very funny stuff here, including crossovers with just about every other fandom you can think of!
A large general fansite for the animated series, with two fanfic archives, one general and one adult, the latter of which is password-protected.