Rat Creature's Journal

Doubt, by ALEO. Gen, Don Eppes. (ca. 8,300 words)
Numb3rs/Supernatural
I recced the previous two stories in this series already (Unexplained and Explained), and this one is a good read too. The Supernatural world functions more as a vehicle for Don-whump than as equal crossover partner in this one, but it's not as if I dislike seeing Don hurt, and angst while he adjusts his worldview to the supernatural.

Unwilling Oracle, by Beatrice Otter. Gen, John Crichton, Kira Nerys. (ca. 1,870 words)
Farscape/Star Trek: Deep Space 9
This has a really cool premise meshing the wormhole mythologies.

Angels in the Architecture , by Davincis_girl. (ca. 12,000 words)
Supernatural/Terminator: The Sarah Connor Chronicles
I think the two universes are a great mix, especially when it comes to the various teenage experiences of growing up with pseudo-military training, and here John Connor travels back to 1999 and gets the teenaged Sam and Dean to help him.

Downloaded series, by Ennyousai. Slash and het, Kirk/McCoy, Scotty/Six. WIP (for the series, the stories are finished)
Battlestar Galactica (2003)/Star Trek: Reboot
I'm not familiar with BSG, but the author's notes said it would work if you just knew ST and it did work great as a Star Trek AU.

The Time Has Come to Be Gone, by Jujuberry136. Gen. (ca. 28,950 words)
Criminal Minds/Supernatural
I enjoy stories with the Criminal Minds team meeting and dealing with the Winchesters, and this one is a good action/case story.

The Mutant Problem, by Katt. Gen. (ca. 7,900 words)
Spider-Man/X-Men
This is a very cool multimedia fanfic in the form of a fictional photo essay by Peter Parker.

Pigs in Spaaaaaaaace, by Kayim. (ca. 2,580 words)
Muppets/Star Trek
How could I not love a crossover between Star Trek and Pigs in Space?

For I Have Been a Stranger in a Foreign Land, by Mortigi_tempo. Slash, Kirk/Spock. WIP (ca. 10,000 words so far)
Dune/Star Trek: Reboot
This is a very cool crossover setup. Kirk and Spock get stranded on Arrakis.

Northern Lights, by Se_parsons. Gen. (ca. 9,700 words)
Supernatural/The X-Files
In this one we get an outsider POV of the Winchester family as Mulder and Scully run into them during an investigation.

To Become Immortal, First You Have to Die, by ShadowLoverK. Gen. (ca. 3,200 words)
Highlander/Star Trek: Reboot
Kirk is an immortal and has his first death from an allergic reaction during the movie.

Abnormal Psychology (ca. 1,440 words) and A Sam Adams Moment (ca. 1,500 words), by Siriaeve. Gen, Sweets, John Sheppard.
Bones/Stargate: Atlantis
Sweets working for the SGC is just an awesome and funny premise.

A Thousand Pages, by Tartanshell. Gen, Scott Summers, Matt Murdock. (ca. 6,250 words)
Daredevil/X-Men
In this Matt and Scott were penpals fo a while as teenagers, then meet again as adults.

Harry Potter

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.

Stargate: Atlantis

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.

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.

Star Trek: Reboot

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.

Supernatural

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.

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.

Stargate: Atlantis

Love Is a Long Long Road, by Hily and Telesilla. Slash, John Sheppard/Rodney McKay. (ca. 40,000 words)
If you like romance mixed with kink this AU is right for you. John and Rodney meet in college, get together and start a D/s relationship (with John as submissive). There are even two endings to choose from, one more fluffy, the other more angsty.

In the Nights When I am Lone, by Vain_glorious. Gen, John Sheppard, Ronon Dex. (2,768 words)
This is a sequel to the Where The Ways Divide, a short role reversal story in which Sheppard is a runner and found by Ronon and his Satedan squad, which I have recced previously. This story explores some more how Sheppard might fare on Sateda.

Black Mountainside, by Whizzy. Slash, Rodney McKay/John Sheppard. (ca. 66,000 words)
I've recced the Black Helicopters series before, but this new novel-length story has been posted since, so I thought I'd point it out again in case you missed it. In this AU Sheppard joined the SGC before Rodney, and then they meet when Sheppard crashes an alien craft in a test flight, and recruits Rodney.

Star Trek: Reboot

An Illogically Beautiful Mind, by Anonymous. Slash, Kirk/Spock. (ca. 5,100 words)
This is a fusion with Good Will Hunting.

A Little Left of Ordinary, by Anonymous. Slash, Kirk/Spock. WIP (ca. 6,300 words so far)
This one is a retelling of the movie in a vaguely steampunkish fantasy setting where magic also works. I really enjoy the worldbuilding so far.

Of Sentinels and Anchors, by Corpus Invictus. Slash, Kirk/Spock. (ca. 13,000 words)
The premise of this one is that Sarek died when Spock was young, so Amanda raised him on Earth and he lacks Vulcan training. As a result Spock has also problems controlling his telepathy. I really liked the Spock-angst and h/c. If you mind the "special mental bond" trope you might want to skip, but in that case Kirk/Spock is probably not your pairing anyway. I however have a soft spot for the same.

Nothing Lay Between, by Dancing Mercury and Jantra. Slash, Kirk/Spock, Pike/Spock. WIP (ca. 43,300 words so far)
Spock is given to Kirk by the Vulcans as a reward. The premise sounds as if it could only work if the setup is in alignment with your kinks, but this one actually has good worldbuilding, gradually gives background for the differences and isn't all that over the top when it comes to changing the characters.

The Hounds of Morrigan, by Hounds_morrigan. Het and slash, Kirk/Spock/Uhura. (ca. 20,000 words)
In this AU Nero was smart enough to destroy Vulcan, Earth and the Federation right away rather than wait for Spock to be able to gloat. The resulting apocafic universe is not that close to canon, but who could resist Uhura, Kirk, and Spock ending up as badass and somewhat traumatized crazy space pirates? It has the additional benefit of working for my slavefic kink and some others. On the flipside, if you don't share my fondness for a variety of non-con and power inequality kinks, you might not enjoy this as much.

Only Good for Legends, by Leupagus. Het and slash, Spock/Uhura and Kirk/Spock. WIP (ca. 19,300 words so far)
This takes place in the Star Trek universe, but Spock has become a police detective on Earth rather than joining Starfleet. I'm enjoying the worldbuilding and the bits of character background that have been revealed so far to explain the changes. It has some angst (the whole cynical detective aspect and some of Spock's backstory) but is also quite lighthearted and funny without being crack or parody.

Time's Divergence, by Logical_stimuli. Gen, Kirk, Spock Prime. (ca. 6,600 words)
This is domestic kidfic fluff that will make you feel warm and fuzzy: Spock comes through the wormhole at the same time as Nero, and because both of Kirk's parents are killed Spock raises Kirk.

Of Pilots And Groundbreaking Inventions, by Misfit_fandoms. Gen, Sulu (though the author labelled it as pre-Chekov/Sulu). (ca. 4,900 words) WIP?
The premise here is the Enterprise as a steampunk ship with an oddball crew. This feels more like a setup rather than an entire story, and the author said there might be more in this universe, but even as it is the atmosphere of this AU is neat and I enjoyed it as it is.

Twice Shy, by Sarka. Slash, Kirk/McCoy, implied Spock/Uhura. (ca. 20,000 words)
Bones is a werewolf, pining after Kirk. I never knew I wanted a Star Trek werewolf fic before reading this, but this was a fun scenario. It's a bit inconvenient to read posted as it is in a comment thread, and I hope the author will repost it elsewhere eventually. (eta: now available in in more convenient format)

Seven Moments, by Barrowjane. Gen. (ca. 1,300 words)
Sandman/Star Trek: Reboot
There's just something about other characters meeting the Endless that I really enjoy, and this example of the genre is no exception.

Down The Rabbit Hole, by Bluflamingo. Slash, Colby/Lorne, Colby/Daniel. (ca. 10,000 words)
Numb3rs/Stargate: Atlantis/Stargate: SG-1
I like how this handles the relationships, the complications that come with dating outside of your secret alien conspiracy, and the way the SGC happens to tangle with the FBI here works for me too.

People Who Repair Quantums, or Five Planets The Enterprise Never Visited, by Ignipes. Gen. (ca. 2,800 words)
Star Trek: Reboot/Alien/Discworld/Doctor Who/Dune/Star Wars
I really enjoyed the crossovers for which I was familiar with the sources, also, while I don't know Discworld, the bit where Spock reacts to the flat disc and giant turtle and so on in space was awesome.

Bright White Light, by lilacsigil. Gen. (ca. 35,000 words)
Supernatural/X-Files
This is set during the X-Files episode "Fallen Angel", which I barely remembered, but the story still worked for me. We get the events of the episode but seen from the perspective (and worldview) of young Sam and Dean. I thought it was really cool how one side believes it's all aliens, and the other it's all supernatural and I was wondering what was really going on. And I liked Sam and Dean adventuring.

Exiles, by nwhepcat. Gen, Oz, Sam. WIP
The premise here is that Sam runs into Oz during Mystery Spot. I found this via Cofax and am really enjoying it so far. The parts are all quite short, but it is updated very often.

a fucking space opera (or Six Characters Who Didn't Board the USS Enterprise), by Oxoniensis. Gen. (3,169 words)
Star Trek: Reboot/Harry Potter/Merlin/Stargate Atlantis/Supernatural/Terminator: The Sarah Connor Chronicles
In the best tradition of wacky crossovers, this was simply a lot of fun.

yahtzee63 just posted the last part of her awesome ST:AOS story Break (Spock/Uhura, ca. 26,000 words), which tells the story of Spock and Uhura's relationship from their first meeting to the end of the movie. You probably have all already read this or bookmarked it for reading anyway, but if not you really should.