EMXC at mulderinjeopardy.org has been out of action for a long time.  The site has been restored at emxc.x-sites.org.
MiJ was in need of some TLC, and has been restored at the above mirror.
Gertie brought us shippers.fredfarm.com for many, many glorious years.  Now that it’s vanished, a copy is available here.
A very talented bunch of fanfic authors have continued on from where MS4 left off.
X-Libris is an ebook library with fics downloadable in epub, pdf or txt versions.
Individual author websites resurrected.
A revived post-FTF and post-episode archive.