YES! Thank you Bastet. :)
I shall start by giving a few links to places where XF fanfiction is being archived, recommended and discussed. I don't know anything about FF.Net, so someone else will have to be the guide for that one. I will keep adding more when I find the time, or when people give new links.
ARCHIVES:
The Gossamer Project
The largest XF fanfiction archive. Contains around 40 000 fics if not more.
Ephemeral
Back in the days if you wanted your fic on Gossamer you posted it on Ephem first. It was a kind of transition place. It used to be linked with Gossamer i.e. stories posted on Ephem would be transferred to Goss but I'm not sure this system is still in place.
A03 - Archive of Our Own
The New Kid. Lovely place. Lots of XF stuff. Great sorting filters.
X-Files Fanfiction
LiveJournal archive.
RECS:
The Reading Group for X-Files Fanfiction
IMO the best place on the net to find great fics. Read a story you're dying to talk about? Want a place where people freely discuss both the good and the bad of a fic in articulate fashion? Then the XF bookclub is for you. There is a master post of stories read and discussed here, though it hasn't been updated in a while.
The Crack Van.
Sadly no longer active. But the archive is still worth checking out.
Haven fanfic folder
I'll be honest, a lot of the stories rec'ed there aren't my cup of tea, but Haven is one of the oldest hub for all things X-Files and the guys who hang out there have an encyclopedic knowledge of X-F fanfiction, which is why I still check it out occasionaly.