I like Alternate Universes in fanfic a lot, so I've collected recs for my favorites in this genre. I read gen, slash, and het in different fandoms, so you'll find all kinds of AUs recced here.
Within a fandom the recs are sorted by author, with new additions being marked. For TS the links are also sorted by the type of the AU (see sub-categories), but in the end I was too lazy to adopt that system for the other fandoms that have accumulated many entries. It is labelled whether something is gen, slash or het, but those are not separate sections. If you are interested in what I think works as AU and what doesn't, or what I count as AUs and what not, and a detailed explanation of what I see as sub-categories and why, you can read my thoughts on these subjects.
Some of my favorite AUs are WIPs, and some of them are probably likely to stay in that state, nevertheless I will also rec those. While I'm not particularly bothered by reading unfinished stuff, I know other people don't like doing that, so I'll indicate in the rec if it's still unfinished.
[Andromeda] [Babylon 5] [Buffy/Angel] [DC Universe] [Due South] [Farscape] [Harry Potter] [Lord of the Rings] [Multifandom] [Numb3rs] [Roswell] [The Sentinel] [Smallville] [Stargate: Atlantis updated ] [Star Wars] [Supernatural] [The X-Files] [X-Men]
Faith Healing, by Aesc. Slash, Rodney McKay/John Sheppard. (ca. 11,300 words)
This AU has a really cool premise. John isn't in the military anymore, but has come across an ancient healing device. Rodney and Lorne track down rogue Ancient tech for the SGC.
Gypsies, Tramps, and Thieves (part one, part two), by Auburn. Gen plot with mixed slash and het elements, John Sheppard, Rodney McKay, Vala, Daniel Jackson, Janet Fraiser, others. WIP
This is simply an awesome space pirates epic mixing both SGA and SG-1 characters, and what's even better is that it reveals us their backstory so that it makes sense that the familiar characters end up this way. It has a great action-adventure plot and I loved the whole atmosphere.
Where the White Lilies Grow, by Eildon Rhymer. Gen. (ca. 44,400 words)
In this AU two alternate realities collide via a Stargate malfunction: a Rodney from an Atlantis that has been cut off from Earth without a Sheppard joining the expedition gets stranded (unfortunately with Wraith too) on an post-apocalyptic version Earth, where he runs into that reality's John Sheppard.
Diplomatic Immunity, by Sarah T. Het, John Sheppard/Teyla Emmagan. (ca. 4,500 words)
I don't want to spoil this, but it is a creepy and disturbing AU premise in which the Athos the expedition encounters is quite different. But it's disturbing in a good way.
Black Helicopters at Dawn (ca. 64,000 words), its sequel Wrong End of the Rescue (ca. 7,000 words) as well as the rest of the Black Helicopters series, by Whizzy. Slash, Rodney McKay/John Sheppard.
Rodney has annoyed the US military too much to become a real part of the SGC, and now tries to prove te existence of aliens the hard way. Meanwhile Sheppard is part of the SGC and crashed an alien craft in a test flight in the Canadian wilderness, and Rodney catches his distress signal. Things unfold from there. I enjoyed this AU a lot, however I've seen several commenters who felt disappointed that there wasn't payoff for the attraction within the story. It really worked for me though.