TrekSites
"Let's see ... Over a period of three days, based on the co-efficient of the number of times a human can reach and sustain a sexual peak..."
"Enough with the calculations already ... come back to bed!"
TOS Fanfiction
Note: Some stories are intended for adults only.  Please pay attention to story ratings if you object to material intended for people over the age of 18.
Djinn's Lair.  Great TOS fiction, focusing mainly on Spock and Christine, but also containing cross-over fiction and other things.
Pat Foley's Fiction Page.  Great TOS fiction, as well as other things!
Gloria's Star Trek Fan Fiction.  Dedicated to Kirk and Spock's friendship with lots of great fan fiction,  both general and adult.
KerJen's Fan Fiction.  Both Star Trek and Star Wars fan fiction. Features Spock and Saavik stories.
Roisin Fraser's Fan Fiction.  Star Trek stories set in the TOS universe as well as Roisin's own Akaren universe.
Saavant's Mostly Vulcan Fan Fiction.  Dedicated to Spock and Saavik.  Lots of good fiction.
Selek's Sarek and Amanda's Lair.  Dedicated to Vulcan's First Family.  Great Sarek and Amanda stories.  Warning -- most are rated NC17.
Spock and Saavik.com.  Dedicated to Spock and Saavik, featuring fan fiction, fan art, book listings, fests, fan made movies, and more.
T'Lin's Trek Fiction.  Mostly K/S stories, but gen Trekfic, as well.  Also has slash stories in TNG, DS9, Voyager and Enterprise.
Where to find Star Trek fanzines...
Empire Books.  Jean Lorrah's home page where you can find "Night of the Twin Moons," Jean's Sime/Jen fiction, and Jean's pro books, including "The Vulcan Academy Murders."
Falcon Press.  Brand new Star Trek zines and classic used zines.
Orion Press. Home to some of the best Trek zines around.
Poison Pen Press. Home to Spockanalia, the very first Star Trek zines, Masiform-D, and many other things.
Waveney Zine Shop/Knightwriter Press.  Literally thousands of fanzines on every topic you can imagine ... a few you can't!
Miscellaneous Trek Sites...
DaisyDownUnder's All Star Trek.  Actually there's Star Trek and a lot more -- Stargate, Andromeda, Harrison Ford, Christopher Reeve and lots more.
The Roddenberry Store.  Formerly Lincoln Enterprises, this is Majel and Rod Roddenberry's site for official Star Trek merchandise and lots more!
Star Trek.com.  The official Paramount Star Trek site!