The Pink Rabbit Consortium -- also has a great links pages here.
Passion and Perfection -- also includes an extensive collection of CSI saffic.
Realm of the Shadow -- large Popular fic section.
Girl Bitz -- hosts saffic, and has a large collection of video from canon lesbian moments.
Girls' Dormitory -- Harry Potter archive.
Mystic Muse -- Jossverse archive, with an emphasis on Willow/Tara.
Wicked and Divine -- a massive Buffy/Faith archive; of variable quality.
Fiction Alley -- the largest Harry Potter archive (scary big, and poorly searchable).
Buffy Fiction Archive -- does what it says on the tin; easy to search.
UnConventional Shipper's List -- also does what it says on the tin (no canon-pairings); unsearchable, organized by author or title only.
Twisting the Hellmouth -- Buffy crossover site; of variable quality.
var [title] -- Anik and Hanibal's site, home of the epic and wonderful Campus [Voyager uber, Janeway/Seven] (plus other stuff).
Novel Expectations -- home to Gina L. Dartt, contains the Just Between Series, and her new Bad Girls stories.
The Written Realm -- Queen Zulu's fiction, mostly Jossverse, mostly Buffy/Faith.
Novel Advice -- general writing advice
Guide to Grammar and Style -- by Jack Lynch, Rutgers University
The Fanfic Symposium -- focuses on multiple fandoms as well as on fandom in general.
Lumos Dissendum -- Harry Potter specific writing help.
Harry Potter Lexicon -- the most complete database for information on the Harry Potter world.
-- extensive information on morality in the Jossverse.