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Ad Astra Fan Fiction Archives
Ad Astra Star Trek Fan Fiction Archive is exactly what it sounds like it is.  Lots of great stuff there and a good community as well.
Ex Astris Scientia banner
Ex Astris Scientia has information on just about everything from the Star Trek universe.  A lot of analysis of Trek stuff from a real world point of view.  Some fantastic in-depth articles on starships can be found here .
Star Trek Expanded Universe is a wiki for fanon projects.  That includes fan fiction, films and RPGs.
Star Trek: Pheonix-X banner Star Trek: Phoenix-X is a script-based fan fiction series that follows the crew of the USS Phoenix-X.  It is more of a humorous series and if you like to laugh it is a good place to go.  It also has a comic series that goes along side with the writing.

Trek Writer's Guild is a site that hosts and links to Star Trek fan fiction.