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] [Merlin updated ] [Multifandom] [Numb3rs updated ] [Roswell] [The Sentinel] [Smallville] [Stargate: Atlantis updated ] [Star Trek: Reboot updated ] [Star Trek: TOS] [Star Wars] [Supernatural updated ] [The X-Files] [X-Men]
Leashed, by Riventhorn. Slash, Arthur/Merlin. (ca. 12,800 words)
The premise here is that Uther doesn't kill all sorcerers but enslaved some. Admittedly slavefic AU with mindcontrol elements is sort of like catnip as far as my kinks go, but this is not a kink wallow.
Sacrifices of the Keeper, by Pygmymuse. Gen. (ca. 28,340 words)
In this AU Don and Charlie's parents are killed in a car accident, when Charlie is still a teenager.
Strangers When We Meet , by Jendavis. Slash, John Sheppard/Ronon Dex. (ca. 14,000 words)
In this AU the expedition encounters a Sateda that didn't fall. I really like how the society was developed here, and seeing different aspects of Ronon.
Take Refuge in What You Know, by Corpus Invictus. Slash, Kirk/Spock. (ca. 118,000 words)
Kirk and Spock are neighbors, and Spock is agoraphobic. Which sounds like a weird premise, but I'm enjoying how their relationship develops here, and the story makes this work.
Walls Burning, Towers Turning, by Leftarrow. Slash, Kirk/Pike. (ca. 5,000 words)
This is a fantasy AU with really neat worldbuilding.
Fighting Gravity, by Pantswarrior. Slash, Kirk/Spock. (ca. 138,700 words)
In this AU Spock doesn't join the Enterprise for its first mission. He and Kirk run into each other on earth afterwards, and this story slowly develops their relationship and reveals the backstory of what happened to Spock.
The Will of the Force, by Verizonhorizon. Slash, Kirk/Spock. WIP
This is a fusion with Star Wars, with Vulcans as Jedi.
My Life's Come Off Its Tracks, by mimblexwimble. Gen. (ca. 28,700 words)
In this AU Dean gets sick as a child, forcing the Winchesters to adjust. We see events from through Sam's eyes and I find good children's POVs really rare, but this one worked for me.