X-MEN
Mutants in love
Vertigo: No Way Up by Kielle is a great example of one of my favorite things about fanfiction, which is when someone takes a minor character and writes an epic which reads like canon.
Kid Dynamo by Connie Hirsch -- This is a classic, and if you started reading the X-books during the period in which it takes place, you'll understand why; I'm rec'ing it despite the heroine's being a Mary Sue, because it's still totally worth reading (and the kind of thing I lived for when I was reading New Mutants in high school back in the eighties). Also, my Electra complex with regard to Magneto should never be underestimated.
All In Your Head by Kristina Sennvik [scroll down]-- This story made me appreciate Psylocke, who I had a hard time warming to after the whole Revanche body-switch storyline... Complex, adult, interesting.
And After the Battle by Alara Rogers -- The best Joseph vignette I've seen.
To Let the Thunder Roll by Kaylee -- Ororo and Yukio that night in Tokyo, this might as well be canon. Also check out her other short Storm piece, Small Cages, and her Kai and Logan series.
X-Manson by D. Benway -- One of the most truly disturbing and original pieces of fan fiction I've ever read.
Alpha by Jane St. Clair and Te -- This is exactly how I always pictured the uh, darker side of Northstar and Aurora's relationship, and when you throw in Nate Grey it's just...really really hot.
Logan's Experiment by O – This is how all Gambit sex scenes should be written (I was willing to suspend my disbelief about the lube, okay? My friends bitch about how he never gets any in O's stories)--that is, with an awareness of the hotness canon tells us is Gambit.
Jump or Fall by Viridian5 -- I just remember reading this and going, Gambit and Nate Grey, why has no one thought of this before?
Diamonds of Ice by paxnirvana --
Meltdown by Maggie the Cat has Logan and Alex Summers hooking up in a Mexican motel room, and how often do you see that pairing written, let alone creditably well? (In the interest of full disclosure: I have a thing for Havok/Alex Summers, especially morally ambiguous or evil AU Alex a la AoA, his stint as Madelyne's Goblin Prince boy toy in Inferno, and Mutant X).
Seventeen by Bishclone
Imaging the X-Men by Jane St. Clair [add rec]
cerebro
CFAN
Fonts of Wisdom
Outside the Lines (mailing list)
Crossroads X
on the road
X-Men: the Movie Slash
more X-Men slash
Alternate Timelines
queenB's Hive
Alykat's World
Thundercrack!
Peeing in the Jean Pool
X-Men 100