Here are some of my favourite X-Files sites. I will be adding to this as often as I can. If anyone has a site to recommend, e-mail me and I'll add a link.
This is my all-time favourite X-Files site. Unfortunately it's closing down, as the High Priestess is moving on to bigger and better things. But, she will be leaving things on the page until she needs the space, so I suggest you go there and read everything before it disappears. I did try to link to her new page, but for some reason it didn't work, so you'll just have to use her link on this page. This site is hilarious, but you have to understand the concept of irony! Especially on her new page ;)
The Church of X members moved to the discussion list here when the COX closed down, so I thought I'd add a link. It's a cool page, great layout and features.
This is the most comprehensive links page for X-Files fanfic that I've found. It has something for everyone, and it's presented very well. I'd be surprised if there was a piece of fanfic which couldn't be found through one of these links. I just wish I had time to visit all of these pages!
This is a cool graphics site. I am a big admirer of Vered's work, and you can see some of it on my site. The banner, X-Files backgrounds and the image on the first page were created by Vered. The site is very impressive, everyone should visit it!