I watched the X-Files for the first time in recent months, and totally fell in love with it. There are a few active-ish communities on LiveJournal (
this is one ). I suspect the main hangouts were mailing lists and newsgroups, though.
They do have a huge fic archive, though:
http://fluky.gossamer.org/ Its layout is similar to the L&C archive, actually, which I love. The main difference is that it does include R and NC-17 rated stories, though. It's also a bit more categorised, likely because it houses something like 35,000 stories.
I didn't even know where to begin at first.
It has a page on FanHistory wiki:
http://www.fanhistory.com/wiki/X-Files (The runners of the wiki site have shown questionable behaviour but it should be pretty accurate, I think.)
Looks like they even had an IRC channel. XD
Julie