Doggett and Scully
Anne Hedonia: X-Files DSR Fan Fiction, SHODDS: Slobbering, Howling, Obsessed Dana-Doggett, The Unnamed Dippett Archive
Mulder and Scully
Agent Chloe's Fanfic, Amy Schatz's X-Files Fan Fiction, Angel's Fanfic, Arcadian Falls' X-Files Fanfic, By Laura Blaurosen, CleverGrrl's Fan Fiction Page, Daydreamer's Den, Details, Donnilee's X-Files Fanfic, dtg's FanFic
Award-Winning X Files Fiction by Deslea
Conspiracy and mytharc stories, many pairing Krycek/Marita and/or Scully/Skinner. Some stories are formatted for e-book readers.
DanaK's X-Perience
Scully-centered stories, including Mulder/Scully and Skinner/Scully romances.
Doggeared - A John Doggett Fanfiction Archive
Gen and adult stories, including Doggett/Scully and Doggett/Reyes romances.
Dragon's Lair
Series featuring Sheryl Martin's original character, Jackie St. George, and Mulder/Scully romance stories.
Fanfiction by Alanna
Pairings include Mulder/Scully, Doggett/Reyes, and Krycek/Scully.
Fanfiction by Plausible Deniability
Humor, Mulder/Scully romance, and the "Young CSM" series about the Cigarette Smoking Man's relationship with Teena Mulder.
Hindi Sad Diamond's World
Gen and het stories in a variety of genres. Includes fan art.
Keep the Faith: X-Files Fanfic Archive
Character-driven stories, including Mulder/Scully romance. Most stories based on season 8.
LJP's Fanfiction Archive
Mulder/Scully and Doggett/Scully stories, as well as crossover stories, favorite quotes, and a contest.
Paranormal Possibilities
Larilyn's stories featuring Scully, Mulder, Doggett, and Reyes.
Philiater's Web
Skinner/Scully stories. Includes photos, wallpapers, wavs, fan art, and story recommendations.
Plop - Humorous X-Files Fan Fiction
A variety of funny and/or irreverent stories, including Mulder/Scully romances. Also offers links to humor authors' home pages.
Primal Screamers
Story recommendations and links to authors' home pages. Also offers a fan fiction primer for readers.
Rachel Anton Stories
Gen and het stories with a variety of pairings. Includes vignettes, romances, and series and post-episode stories. Also offers recommendations.
Sheena
Mulder/Scully romances, angst, and humor by Sheena.
Skinner/Scully Romance Archive
Adult stories featuring Walter Skinner and Dana Scully by various authors.
The Avalon Foundation
Gen and het stories are mostly Mulder/Scully and include a selection of collaborations between Avalon and Marie Endres.
The Dark Place
"This is the fanfic your mother warned you about." A variety of het stories, most of them Mulder/Scully, but other pairings include Scully/Krycek and Skinner/Other.
The In-Box
Stories focusing on Doggett, including case files and romances with Scully and other characters.
The Shippers Who Like Doggett Fic Archive
Stories portray Doggett and Reyes in a positive light while preserving Mulder/Scully romance.
Through the Looking Glass - Fanfic and Recs by Mai
Stories focus on a variety of characters; also includes some Mulder/Scully romance and post-colonization stories.
TXF Sayanora Support Group FanFics
Mostly Mulder/Scully romance stories, but also includes humor, poems, and stories featuring some other pairings. All stories are reviewed by one of the archivists.
X-Fic
Analise's Mulder/Scully romance stories, as well as recommendations.