These are just a few of the original sites I'm aware of that are still online. The ones listed below are mostly non-free-host sites; there are also remnants of those around.
The wonderful Mimic117 has preserved a massive number of them over at xphilefic.com:
Sadly, very few of the remaining sites are still updated, and some of the authors are no longer with us. I've marked the ones that are sometimes updated with a violet coloured border. Most of these banners are from the sites themselves or made using components found at the sites.
Gertie's Shipper/Angst archive has been restored & code upgraded. MiJ was brought back to life with a responsive code upgrade.EMXC is complete, but still requires cosmetic surgery.The CRF: A revived post-FTF and post-episode archive.AEA disappeared multiple times but is back at aea.x-sites.orgCOLB is dedicated to everyone’s favourite doof, Agent Pendrell.The Socks Shoppe: a small Pendrell slash archive.A very talented group have continued on from where MS4 left off.X-Libris is an ebook library of classic fics.
MORE ARCHIVES AVAILABLE ELSEWHERE:
Gossamer: The ultimate archive, all types of fic.The Annex: X-Files novel archiveAll the specialised archives managed by mimic117Whispers of X - Sexytimes archive.Over 10 years of X-Files case files and themed stories, many exclusive.A revision and rewrite of Season 8Neoxphile's archive of all fics scary.Neoxphile also hosts the Nursery Files at Mulder's Creek.Christine's collection of IWTB, S10 & 11 Fanfic. Still running on Tripod!.Fugues in the Key of X archive & moreWorld of X: German fanfic and translations.RaTales Krycek archive, currently at squidge.org. Some of the other sites you'll find at squidge.org (mostly slash)SquidgeWorld: The slash version of AO3
The main archives that most authors currently use (Multi-fandom):
AO3: Where you'll find most current fanfic for every fandom.Fanfiction.net: Not as popular but still home to some good stories.
OTHER X-FILES SITES:
Need help figuring out what happened when? (I'm looking at you, CC).Ask here for that fic you can't find.Bluray episode images captures. Also the David & Gillian image archive.Screencaps from all eps + Millennium + Monk.InsidetheX: Transcripts for almost all episodes.All sorts of goodies.Lists of fics by category, cover art & digital image manipulations.X-Files Resources - Bulk downloads, fonts,
This site is dedicated to the early authors of TXF fan fiction who set the bar so high, and to the current generation of authors who continue to raise it. Those who fit into both categories deserve triple the dedication.
I also want to dedicate this to the original webmasters/mistresses and archivists, who may or may not have been the authors themselves.