These are Links to some of the best sites out there.  They're divided up, so it should be pretty easy to find what you want.  If you find a link that doesn't work, be sure to send me an email so I can fix it.  Enjoy!  :)
Sites where you can find great fic.

The Gossamer Project - Pretty much every fanfic on the net that is archived is archived at this site.  You can search by author, by genre, by title, and even by spoiler.  If you've got something specific that you're looking for, go here first.

Ephemeral - All the newest stories- they're here as soon as they're posted.  If you're looking for the newest stories out there, check this site out. 

Alternate Season 8 - Season 8 revisited.  A series of fanfics based on the episodes in season 8, but slightly different.  Better.  Read them, you'll get addicted, I promise.  :)

ATXC -, the ultimate X-Files fanfic newsgroup.  (This link may only work for aol users- you'll have to check with your isp for a way to connect to newsgroups.)

Fic Scouted - A page of favorite fics scouted by the page's owners.  Good stuff!  Updated weekly.

Char Chaffin's Fanfic - A great author- read them all!  I command you!  :P

Whispers of X - Smut.  Woohoo!  :)  No one under 17- this is all NC-17 fanfic.

The Annex - Site for novel length fiction.  Great if your looking for a nice long read. 
Sites with a purpose.

The X-Files - The Official Site.  They have a *real* episode guide, pics, news, info about fan mail, etc.  A great place to start. (And it's legal!!)

Haven for the FBI's Most Unwanted - A great Mulder/Scully based site with news, fanfic, a HUGE image gallery, message boards, and pretty much anything else you could ever want from a Mulder/Scully page.

Beta Reader's Circle - An organization for beta reading- if you want to become a beta reader or want your story betad, this is the place to go.

X-Files Institution for Relationshippers - I love this site. Set up like a mental institution, for all us crazy 'Shippers.  Visit the moments in history ward, or discuss "dealing with discrimination," or visit the "visual stimulation" page for some great pics.

The X-Files Shrine - A great multimedia archive of pics, sounds, and video.

The X-Realm: Multimedia - Did you miss one of the XF stars on a late night talk show?  On Entertainment tonight?  This site has video of just about every XF star's appearence on talk shows, entertainment shows, etc. as well as some other great multimedia stuff.

Relationshippers:  The X-Files Search Engine - Looking for a shipper site?  Check this webpage out, it's a pretty comprehensive search engine.  Lots of pages.  Lots and lots of pages.  :)

Road Runners X-Files - A really comprehensive general site with tons of episode screen grabs, message boards, etc. 
Fan Sites
Sites with no purpose.  Just kidding.  These are other sites like mine where you can find fun and useful info, pics, more links, etc.

E's X-Page - A great site with pics, fanfics, postcards, etc.

Je Souhaite - ::Sigh::  A site so much better than mine, it's sad.  :)  Really, it's great though.  Tons and tons of stuff, and the layout of the page is gorgeous.

Mulderisms and Scullyisms - Great quotes from Moose and Squirrel.  Updated through season 8.

Rohan's X-Files Realm - This page is incredible.  So much stuff... multimedia, postcards, episode guide, transcripts, and pretty much anything else you could think of.  Non-Shipper though.  (Not anti-shipper, just non-shipper)

Imajiru - I suppose I could have put this under fanfic, but I didn't.  Oh well.  Imajiru is the author of "Taming the Unicorn" (one of my most favorite fanfics of all time) which is not archived at any of the main sites anymore, but you can find it here!  Check out her site and her fanfic, it's all great. 

Jamie's Site Directory - Whispers of X (NC-17 fanfic), the Priceless Archive, and a Shipper site (fanfic and collages).  Check it out.
Sites that are completely random- but cool!  :)

Why did the chicken cross the road? - The answer to the eternal question, X-Files style.  :D
Non X-Files
Pretty self explanitory, n'est-ce pas?

SmallvilleFan - A totally awesome Smallville site.  Pretty much everything you'd ever need to know about the show.

Smallville News - All the newest info on Smallville.

The Smallville Ledger - This is seriously one of the coolest sites I've ever seen- it's a fake newspaper from the show, but it follows the show's storyline by episode and it has real newspaper articles.  Well, real fake newspaper articles.  :) 

The Smallville Torch - Same as the Leger, but the High School Newspaper.  I can't get enough of this, it cracks me up.