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 updated ] [Lord of the Rings] [Multifandom] [Numb3rs] [Roswell] [The Sentinel] [Smallville] [Stargate: Atlantis updated ] [Star Trek: Reboot updated ] [Star Wars] [Supernatural updated ] [The X-Files] [X-Men]
House Colours, by Sarka. Slash, Harry Potter/Draco Malfoy. (ca. 12,800 words)
This is a Slytherin!Harry with Gryffindor!Draco AU, and I really enjoyed it, not least because it had a Ron who was first friends with Draco and then Harry, rather than the Ron-bashing that is so depressingly common in Slytherin!Harry stories.
Snakeheads: A Love Story, by Leah. Slash, Rodney McKay/John Sheppard/OMC. (ca. 17,600 words)
I never really expected to read a John/Rodney/Goa'uld threesome, but this was written by Leah, so of course I gave it a try, and wasn't disappointed. This one was far more fun than you'd expect with this setup.
The Little Sister, by Martha. Slash, Rodney McKay/John Sheppard. WIP
I like film noir AUs, and ever since Vegas I like seeing Sheppard as down on his luck detective even more, but what makes this AU great is that the alternate reality is still based on Stargate. The setup is really intriguing, and I like that in it the Goa'uld were smarter in their take over of earth, smart enough that the majority doesn't even think of them as bad guys.
Strange Aeon, by Slybrarian. Slash, Sheppard/Mitchell, Sheppard/Lorne. WIP (ca. 32,000 words so far)
How could anyone resist a mix of Lovecraftian space monsters and with Stargate? The series is still a WIP, and I'm really enjoy how this is subtly different from canon, and the world building and hints of mythology so far have me hooked. And I like Cam in Atlantis.
Where the Brave Dare Not Go, by Telesilla. Slash, John Sheppard/Rodney McKay. (ca. 18,500 words)
It's of course no secret that I love were-animal stories in general but this one is awesome. I liked the sense of hinted backstories in the AU for the characters, and that the universe seems larger than what's in the story. And I liked that the Were mythology of this universe wasn't magical or really supernatural(at least not from what we learn of it), but seemed almost mundane (in a good way) in the way the society deals with this.
To the Wide Outposts (ca. 7,490 words) and The Known From the Unknown (ca. 12,000 words), by Vain_glorious. Gen, Ronon Dex, John Sheppard.
I've recced the other two stories in this series (Where the Ways Divide and In the Nights When I Am Lone) already, but in case you missed these two that have been posted since my last recs update, it doesn't hurt to point the 'verse out again. In it Sheppard has been made a runner by the Wraith and is found and taken in by Ronon and his Satedan squad.
As You Are, by 13empress. Slash, Kirk/Spock. (ca. 10,700 words)
I don't often rec PWPs, but this one has a really cool perspective, in that it is alien-kink, but from Spock's POV, so the humans are the ones looked at through the xenobiology lense. The AU premise (though I guess it could converge with canon) is that before Spock attends Starfleet Academy he wants to have a human sexual experience, as he has heard all kinds of things about human sexuality. So he spends a day with rentboy!Kirk. It's not humor, but not extremely angsty either.
Open Up My Eager Eyes, by June. Slash and femslash, Kirk/Spock, Uhura/Gaila. (ca. 15,000 words)
This is a fusion with Pump Up the Volume that was written for reel-startrek. I really enjoyed this, even though I'm not particularly into high school AUs or into making Spock a human/loosing the SF elements in Trek fiction.
Lensflare Lover, by Leftarrow. Het, Pike/Enterprise, Pike/Number One. (ca. 7,300 words)
This has a cool premise in which the spaceships have avatars.
In Truth, by Mint_amaretto. Slash and het, Kirk/McCoy, Spock/Uhura. (ca. 3,570 words)
This is a really creepy, twisted AU, as any mix with the Dollhouse concept (not the series itself, more the basic premise) should be.
The Sky Was Made for Us Tonight, by Waketosleep. Slash, Kirk/Spock. (ca. 5,500 words)
In this AU Vulcans decided to supervise humanity more closely, and Kirk and Spock are delinquent rebels together after meeting in a holding cell and staging a prison break. I enjoyed this scenario a lot.
An Illogically Beautiful Mind, by Waldorph. Slash, Kirk/Spock. (ca. 8,215 words)
This is a fusion with Good Will Hunting. (Now expanded into a longer series.)
Untitled SPN Snippet, by Cofax. Gen. (ca. 1,300 words)
I wanted this to be longer and an apocafic epic rather than a snippet, but the world building was still interesting.
Teufelshunde, by July. Gen. WIP
In this AU Sam and Dean grow up with a foster parent after John has been arrested. I really like the OC and the structure with the flashbacks here works for me, even though flashbacks aren't my favorite things.
Rain Falling Down, by Maychorian. Gen, Bobby, Castiel, Jimmy, Dean, John. WIP (the series, individual stories are finished, ca. 20,000 words so far)
In this AU Castiel travels back in time to prevent the apocalyse, but things go wrong and he gets stuck in his host as a kid without his full powers, and lots of angst and h/c ensue.
And Burn the Long-liv'd Phoenix in her Blood, by Tabaqui. Gen. (ca. 6,800 words)
In this AU Mary survives, but they still hunt. I enjoyed the setup and look at their lives.