X-Files & The Real Ghostbusters
Imajiru

Highlander & Supernatural & Star Trek
Killa's Adventure in Melodrama

Due South, Sentinel, Highlander & X-Files
Barb's Multi Fan-Plex

Smallville & Sentinel
Lenore's Stories

Buffy & Smallville
Witlingville

Multi Archive
The Archive at the End of the Universe

I have been reading lots of different fandoms, so:

The Insomniac's Playground
Smallville

The Erotic Fiction of Becca Abbott
Anime

Purna's Fiction
Due South & Smallville

Changes in Latitudes
Due South

Fierce Flawness (at least I hope that is the site's name)
X-Files, Due South etc.

Kirk/Spock Fanfiction Archive