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Geocities.com has 82,735 URLs listed in 49,956 Dmoz categories.

Beehive
Gen and adult stories starring Marita Covarrubias.
http://www.geocities.com/Area51/Zone/2959/beehive.html
Top/Adult/Arts/Online_Writing/Fiction/Fan_Fiction/Television/X-Files,_The

WalterTorture
Slash, adult het, gen, and humor depicting the torment of AD Skinner.
http://www.geocities.com/Area51/Shadowlands/7855/index.html
Top/Adult/Arts/Online_Writing/Fiction/Fan_Fiction/Television/X-Files,_The

155 Words
Very short stories, including Mulder/Scully and Scully/Skinner romance, Mulder-torture, slash, and portrayals of Spender. Submissions welcome.
http://www.geocities.com/Area51/Stargate/4580/
Top/Adult/Arts/Online_Writing/Fiction/Fan_Fiction/Television/X-Files,_The

IOHO - In Our Humble Opinion...
The best stories out there, according to Lisby, iwonder, Logovo, Sapphire, and Xanthe. Also includes image galleries, copyright information, and works in progress.
http://www.geocities.com/Area51/Shadowlands/5318/
Top/Adult/Arts/Online_Writing/Fiction/Fan_Fiction/Television/X-Files,_The

Bill Scully Fanfic Archive
Gen, adult het and slash stories featuring Bill Scully.
http://www.geocities.com/Area51/Shire/2390/
Top/Adult/Arts/Online_Writing/Fiction/Fan_Fiction/Television/X-Files,_The

CharlieFic - An Archive for the Forgotten Scully
Gen, het, and slash stories that feature the youngest Scully brother, who has never actually appeared in the series.
http://www.geocities.com/charliefic/
Top/Adult/Arts/Online_Writing/Fiction/Fan_Fiction/Television/X-Files,_The

CounterMeasures - The Lone Gunmen Fanfiction Archive
Includes stories based on both the X-Files universe and that of the spinoff series.
http://www.geocities.com/lgmfanfic/
Top/Adult/Arts/Online_Writing/Fiction/Fan_Fiction/Television/X-Files,_The

The Naked Eye
Gen, het, and slash, mostly post-colonization works or stories based on Mulder's abduction and Scully's pregnancy.
http://www.geocities.com/nakedeyerecs/
Top/Adult/Arts/Online_Writing/Fiction/Fan_Fiction/Television/X-Files,_The

Dot's Den
Mulder/Skinner, Skinner/Scully stories and drabbles.
http://www.geocities.com/Area51/Aurora/3142/index.html
Top/Adult/Arts/Online_Writing/Fiction/Fan_Fiction/Television/X-Files,_The/Authors

I Believe - The X-Files Fanfiction of Diana Battis
Gen, het, and slash stories, including romance, post-episode, humor, and angst.
http://www.geocities.com/Area51/Vault/4090/TheXFilesFic.html
Top/Adult/Arts/Online_Writing/Fiction/Fan_Fiction/Television/X-Files,_The/Authors