Fonts of Wisdom
This initially grew out of Luba Kmetyk's obsession with Pryde and Wisdom pairing, and expanded exponentially into one of the best 'for grown-ups' X-Men archives (and Spike archives) out there. Her selections tend to be a bit much on the sturm und drang side for me, but it's pretty much uniformly beautifully written. Luba split the archive into lots of categories, so look for the good authors on every page. I can barely put my foot in the door here -- there's too much. Look for Tag Team, DuAnn Cowart (the awesome Just Lucky, I Guess), Susan Crites, Phil Foster, Connie Hirsch (the classic Kid Dynamo), Luba Kmetyk herself (warning: although Luba is excellent, unflinching, and gives great smut, she has a nasty habit of not finishing stories), Mel, Melissa, and Amanda Sichter (Remember, When Falling). Updated link

Dyce's Fic
Look for anything Dyce has written, although it's scattered across many archives (Fonts of Wisdom and ComicFic.net have much of it). Particular Recommendations: Generation Cat (link to first story), Rising Sun, The Song Title Series, Maturity in B Minor, Godless Annie (look for Dyce on the page), her poetry -- but I honestly don't think she knows how to write anything that isn't good.

Home to one big archive and many smaller archives dedicated to the movieverse -- and this pairing in particular -- you'll find a lot of really well-written fic here. I'm not particularly into the Logan/Rogue ship, and even I like some of this stuff. The Insomniac Playground and Detritus are your two best bets.

A compiliation archive that used to be the Itty Bitty Archives. Largely angstfic, but also largely well done.

Shifting Sands
Via the Wayback Machine. Defunct, but still a pretty good archive, best known for being the home of the X-S: Growing Up X series about young Sikudhani McCoy.

Tie Me Down by MsSolo
There are reasons I stopped reading X-Men, and I'm really glad I did, given what they did to one of my favorite characters. But MsSolo takes Jubilee and plunks her down in London with an equally destroyed Jono, and the resulting relationship is just wonderful. Long and detailed and a little dark, with unshakeable POVs from both Jubilee and Jono. Call it PG-13 for language and sex. Gorgeous.

Two Pair by L.M. Griffin
One of the series' that started the Gambit/Jubilee pairing; it works. Link to Wayback Archive.

Insane Musings
Jaelle and Orla aren't my favorite writing team, but I'll give them massive, massive props for their side-splitting and epic Generation X Presents: A Short (and somewhat inaccurate) History of the X-Men. On a rainy day, Generation X decides to amuse themselves with a little presentation....