Single Fandom Archives

A list of Notable Fanfiction Archives. The only requirement to be on this list is that it only covers one fandom. Multi Fandom Archives, naturally enough, go on Multi Fandom Archives.

Ace Attorney

 * Objection!

Adventure Time

 * The Last Human

Animorphs

 * The Animorphs Fan Forum: Though not exclusively devoted to fanfiction, this forum boasts a considerable archive.
 * Cinnamon Bunzuh
 * Six Days the Animorphs Were Idiots

Babylon 5

 * Jumpnow

Beyblade

 * BeyFanFic Central

Civilization

 * Civ Stories and Tales
 * Civ5 Stories and Let's Plays
 * Civ4 Stories and Tales
 * Civ3 Stories and Tales

Club Penguin

 * Club Penguin Fanon Wiki

Daria

 * Outpost Daria's Fanfiction Archive

Die Hard

 * Viciouscats' Master List of Die Hard Fanfiction: As of 02/28/2009, holds about 227 stories pertaining to the Die Hard franchise, including but not limited to slash, het, gen, AU, etc.

Doctor Who

 * A Teaspoon and An Open Mind (link)

Elfen Lied

 * ElfenLiedFanSite.com: A forum post website for fans of Elfen Lied.

Eureka

 * EUReKA Fanworks

Gravitation

 * Gurabiteshiyon.net

Gilmore Girls

 * Black & White & Read

Glee

 * GleeFic
 * Scarves & Coffee: A Kurt/Blaine-only archive.

Halo

 * Halo.Bungie.Org Fan Fiction (HBOFF)

Harry Potter

 * DarkLordPotter.net: A site dedicated to high quality Harry Potter fanfiction of all kinds. Usually leans towards darker stories, as the name suggests, but it's not exclusively devoted to that genre.
 * HarryPotterFanfiction.com: The oldest and biggest Harry Potter fanfiction archive.
 * Fiction Alley: Active since 2001 and famously founded after the Cassandra Claire plagiarism debacle.
 * Lumos: A quality fandom archive with sub-archives for various HP characters.
 * Simply Undeniable: A Hermione/Ron, Harry/Ginny archive.
 * Ginny Potter.com: Mostly Harry/Ginny, but hosts other Harry Potter fanfiction.
 * PhoenixSong.net: An archive for canon pairings, mainly Harry/Ginny and Ron/Hermione.
 * The Quidditch Pitch: A general fanfic archive.
 * The Unknowable Room: A general fanfic archive created and populated mainly by James/Lily writers.
 * Sink Into Your Eyes: Again, mostly Harry/Ginny.
 * / Fire and Ice Archive: An archive exclusively for Draco/Ginny fanfiction.
 * Potions and Snitches: An archive for fics featuring the gen relationship between Snape and Harry. This archive bans all Harry/Snape Slash (but accepts slash of other kinds so long as the primary focus of the fic is Harry and Snape's gen relationship) and all MA rated fic.
 * Portkey: A Harry/Hermione, Ron/Luna, Draco/Ginny, and Lily/James fanfiction archive, though the first makes up most of the stories on the site.
 * The Hex Files: A Harry/Draco slash and gen archive. Other pairings/couples/etc are allowed, but the focus has to be Harry/Draco.
 * The Silver Snitch: An archive for any and all Harry Potter slash. Mostly Snape/Harry and Draco/Harry fics, but there's others too.

House MD

 * The House Fanfiction Archive: All genres of House fanfiction; must be 18+ to view the full site.

Iron Man

 * Tony and Pepper

Joss Whedon

 * Buffy Fiction Archive: Buffy the Vampire Slayer and Angel fanfiction archive.
 * The Buffy/Giles Fanfiction Archive: A Buffy archive for Buffy/Giles fics.
 * Firefly Links: A list of Firefly archives.
 * Dollhouse Wiki: A fanfiction archive for Dollhouse.
 * Land of Denial: This archive is full of Buffy/Angel fan fics. It has not been updated since 2005 but it's still huge and really good.
 * BuffynFaith: A Buffy archive for Fuffy. Pretty big and still going strong.
 * Scribes of Angel: Over 800 fics and growing. They are hand picked for greater quality.

Kuroko no Basuke

 * shootswishscore: Membership is required to view the various fanfics, but absolutely anyone is welcome to join.

Lord of the Rings

 * Henneth Annun: One of the oldest and largest LOTR fanfiction sites. Has a slow server, unfortunately.
 * Faerie
 * West of The Moon: A hobbit-centered archive.
 * Stories of Arda: An archive with a focus on het and gen. Does not allow NC-17 works.
 * Library of Moria: A slash-only archive.
 * The Mellon Chronicles: An archive of fanfiction centered around the friendship between Legolas and Aragorn, emphasis on friendship as there is no slash to be found. The owners are no longer accepting fanfiction to the archive.

Lois and Clark

 * The Lois & Clark Fanfic Archive

Lost

 * LostFic

My Little Pony Friendship Is Magic

 * FIMFiction

Naruto

 * TONFA

Neighbours

 * Neighbors

Order of the Stick

 * The Crack Pairings Thread

Phantom of the Opera

 * The Fifth Cellar

Pokémon

 * AGNPH Fiction: Site is NSFW, be warned.

Psych

 * Psychfic

Red vs. Blue

 * RvB Society

Repo! The Genetic Opera

 * Repo! The Genetic Archive

Silent Hill

 * Silent Hill Fanfiction Archive

Stargate

 * Heliopolis
 * The Alpha Gate: For Stargate SG-1.
 * Atlantica: For Stargate: Atlantis.
 * Wraithbait: Another Stargate: Atlantis archive.
 * Stargate Novel Archive: Compiles long SG-1 fanfiction.
 * Sam and Jack: An archive for Sam/Jack shipper fiction.
 * Area 52: A huge Stargate slash archive, for SG-1 and Atlantis. Mostly Jack/Daniel and John/Rodeny.

Star Trek

 * Trekiverse
 * KSArchive: An archive solely for Kirk/Spock fanfic, from both the original series and the new movie.
 * Warp 5 Complex: A Star Trek: Enterprise fanfiction archive.
 * Ad Astra

Star Wars

 * KotOR Fan Media: A fanfiction archive for Knights of the Old Republic.
 * The Force.net

The Beatles

 * Rooftop Sessions

Super Mario Bros.

 * Lemmy's Land: A fanfiction archive (which also features Fan Art and Web Comics), all about the Mario world.

Tamora Pierce

 * The King's Own

That Guy With The Glasses

 * The Secret Treehouse

The Thing

 * Outpost #31 Fan Fiction Library

The West Wing

 * The National Library

The X-Files

 * The Gossamer Project

Titanic

 * Anne's Story Page

Total Drama Island

 * Total Drama Fanfiction

Touhou Project

 * Patchouli's Scarlet Library

Warcraft

 * The Scrolls of Lore Fanfiction Forum

X-Men

 * X-Men Hero: Cyclops: The fan fic archived dedicated towards X-Men's Leader Cyclops.