General Archives

Gossamer Skinner - The mother-of-all fan fiction archives.
Gossamer Fluky - A mirror site of the mother-of-all archives.
Gossamer Krycek - Ditto.
Gossamer FTP Archive - Ditto, and then some.
Ephemeral: The Auto-Archive - Get the latest stories from the XFF list and from AXCT, hot-off-the-presses.
FanFiction.net - A general site for fan fiction, which includes a category for The X-Files.

Specialized Archives

The Romantic Fan Fiction Archives
Mark of X-Cellence Award Winning Fan Fiction
One in Five Billion: A Fan Fic Review Site
Clinique's Chaos Hidden Gems
The Basement: The best of X-Files Fan Fiction
The Primal Screamers

Informational Sites

Deep Background - Information about episodes, FBI protocol, medicine, etc.

Authors' Sites

Rachel Anton
Lydia Bowers' Fan Fic Page
Barbra D.
Anne Haynes' (Paula Graves_ Homepage
Leyla Harrison's Fan Fic Page
Juliettt's X-Files Fan Fic Page
Dasha K's Fan Fic O'Rama
Kipler's Fan Fic Page
The Ladies of Monday Night Fan Fic Archive
CiCi Lean's Fan Fic
Sheryl Martin's Dragons Series Fan Fic Page
Birgit Mueller's Fan Fic
Madeleine Partous' Fan Fiction Stories Homepage
Sheryl Martin's XF Fic
Marguerite's Fan Fic
Punk Maneuverability's Homepage
Dawson Rambo's Fan Fic Page
Jill Selby's Page
Jennifer Stoy's Creative Corner
Xscout's Hollow