Video game series which do not yet have enough sites to merit their own subcategory (or which I haven't gotten around to separating yet) can be found here.
Animeaddiction's Page Mark IV
Categories: Ranma, Other Anime, Bubblegum Crisis, Other Video Games, Fighting Games, Robotech
Story Count: 36
Comments: Home of, among many others, the Ranma stories "Dual Destinies," "Fighting Blind," "The Great Crossover Crisis," "Cat Fist Fury," the Ranma/Tekkaman Blade/Vandread crossover "Tekkadread," and the Ranma/Pokemon crossover "Fist of the Pikachu."
7/3/06
Another Random Website
Categories: Other Video Games, Fighting Games
Story Count: 4
Comments: Castlevania, Guilty Gear and Samurai Showdown fiction. Site last updated in August 2000.
7/3/06
Capcom Strike Force
Category: Mega Man, Other Video Games
Story Count: 2
Comments: Series of stories featuring seven heroes from Capcom games. Last updated in July 2004.
7/18/06
The Castlevania Dungeon
Category: Other Video Games
Story Count: 35
Comments: Site devoted to the Castlevania series. Fanfiction is divided and organized by genre.
5/30/05
Casual Villain
Categories: Square-Enix, Other RPGs, Other Video Games
Story Count: 16
Comments: Final Fantasy VII and Vagrant Story are the predominant fandoms
6/11/04
The Crash and Partners Storycenter
Category: Other Video Games
Story Count: 230
Comments: Mostly Crash Bandicoot fanfic, with a smattering of other fandoms. Archived by author, with three pages listing (see the "More writers..." and "Even more writers..." links). Last updated in May 2003.
6/18/04
Daniel J. Drazen's Sonic Page
Category: Other Video Games
Story Count: 30
Comments: Sonic fanfic, based for the most part on the comic series.
7/1/04
Fantasm Soldier's Temple
Categories: Phantasy Star, Lunar, Other Video Games
Story Count: 12
Comments: Home of the Phantasy Star/Valis crossover "The Fantasm Swords" and its Lunar/Alisia Dragoon companion, "The Lost Dragon of Lunar."
7/18/04
From the Desk of Tiarra
Category: Other Video Games
Story Count: 2
Comments: Sonic fanfic found in the poetry/prose section.
8/1/04
The Game Fan Fiction Collection
Categories: Fighting Games, Square-Enix, Other Video Games
Story Count: 60
Comments: Tekken, Bloody Roar, and Final Fantasy have the lion's share of the stories here. Last updated in May 2003.
8/7/04
Gameforms
Categories: Square-Enix, Other Video Games, Other RPGs, Phantasy Star, Xenosaga
Story Count: 280 authors
Comments: Fan fiction is found under "Interact."
8/7/04
Herald's Rest
Categories: Ranma, Sailor Moon, Comics, Fighting Games, Other Video Games
Story Count: 6
Comments: Home of the Ranma/Sailor Moon crossover "Forgotten Time." This site is no longer being updated.
5/30/05
IcyBrian's RPG Page
Categories: Square-Enix, Other RPGs, Xenosaga, Suikoden, Lunar, Phantasy Star, Other Video Games
Story Count: 800+
Comments: One of the largest RPG fanfic archives remaining in existence. About half the stories here are Chrono Trigger fanfics.
8/26/04
Joshua Dyal's Fanfics-n-Stuff
Categories: Fighting Games, Other Video Games, Ranma
Story Count: 3
Comments: Home of the Street Fighter 2 story "War For the Worlds." Last updated in October 1998.
9/15/04
Lex's Page
Categories: Cartoons, Other Video Games, Mega Man, Suikoden, Other Anime
Story Count: 12
Comments: The link to most of the Transformers stories ("tf fan") is broken.
10/2/04
Marik Central Command
Categories: Square-Enix, Other Video Games
Story Count: 9
Comments: Home of the Final Fantasy VII story "Forgotten Messiah" and sequels. Last updated in May 2003.
1/14/05
Melodie's Storycenter
Categories: Other Anime, Voltron, Ranma, Cartoons, Sailor Moon, Other Video Games
Story Count: 70
Comments: Last updated in January 2002.
1/14/05
The Metroid Database
Category: Other Video Games
Story Count: 35
Comments: As the name suggests, this site is devoted to the Metroid series. Most stories archived here are in .doc format.
5/30/05
The Ninja Gaiden Homepage
Category: Other Video Games
Story Count: 4
Comments: Home of "Ninja Gaiden III: The Fury of the Dragon."
5/24/05
Sonic HQ
Category: Other Video Games
Story Count: 89
Comments: Fanfic located under "Fan Fair," arranged by author.
7/15/05
Victar's Tekken and Mortal Kombat Fanfic Archive
Category: Fighting Games, Other Video Games
Story Count: 10
Comments: Home of the Tekken 2/Mortal Kombat 3 crossover "Ashes of the Phoenix."
12/23/05