Black Queen Phoenix
Fan-fiction archive primarily based around Jean "Phoenic" Grey-Summers. Site has content ratings and offers some images and links as well.
FanFiction.Net: X-Men
A vast array of X-Men stories including various characters from all the titles.
Project: Marvel
This new site features fan-fiction based on X-Men and X-Force and is looking for submissions.
The Wolverine and Jubilee Page
Wolverine and Jubilee see particular focus, both indivually and together, on this site which also offers character backgrounds, pictures and links. A few other X-Men characters also have stories included.
The X-Men Zone
Includes categorized, X-Men based stories. Welcomes submissions.
Wolvster FanFiction
This newer fan-fiction archive is based around Wolverine.
X-Men Hero: Cyclops
Cyclops stories along with some background information, pictures and links.