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.

Nothing Like Billy, by Embroiderama. Het, Ellen Harvelle/Fox Mulder. (ca. 2,622 words)
Supernatural/The X-Files
There isn't much plot beyond the sex in this crossover, but there was enough characterization and a plausible reason for their meeting to not have the story feel arbitrary.

Leapin Lizards, by Gwendolyn Grace. Gen, Sam Winchester, Dean Winchester, Sam Beckett, Al Calavicci. (ca. 18,560 words)
Quantum Leap/Supernatural
Sam Beckett leaps into John Winchester when Dean and Sam were still children. There is a good case story, and Beckett has to deal with finding out that the supernatural is real, and handle two young Winchesters.

With a Bang, by Mink. Gen, Alec, Dean Winchester, Sam Winchester. (ca. 42,000 words)
Dark Angel/Supernatural
This is a good action-adventure, and I liked how the shows' mythologies were meshed, even though I'm not that into the whole breeding cult arc of DA season two. Also Alec, Sam and Dean together are just fun to watch.

Curiosities (ca. 4,045 words) and Stutter (ca. 1,500 words), by Penknife. Slash, Erik Lehnsherr/Charles Xavier, Tom Riddle, Lily Potter, Sirius Black.
Harry Potter/X-Men
Recently Penknife offered to write timestamp fic, and I noticed that I never recced the original crossover for which I requested a timestamp. Anyway, in the first Erik Lehnsherr encounters Tom Riddle in 1950, the timestamp is set during the first Voldemort war/the Marauders era, and both are interesting and well worth reading.

Brothers in Arms, by SylvanWitch. Gen, Dean Winchester, Derek Reese. (ca. 2,440 words)
Supernatural/Terminator: The Sarah Connor Chronicles
Dean runs into Derek while hunting, and somehow these two shows just go together like chocolate and hazelnuts.

What Kind of Day Has It Been?, by Victoria P. Gen, Dean Winchester, Sam Winchester, Kermit and the Muppet Show ensemble. (ca. 3,300 words)
Muppet Show/Supernatural
I love Muppet crossovers (felt rules! *g*), and this one made me laugh a lot.

Winchesters at Hogwarts series, by Ignipes. Gen. (so far three stories with ca. 10,400 words)
Harry Potter/Supernatural
In this crossover AU John dies and Sam and Dean are sent to wizard relatives in England, so Dean attends Hogwarts.

And All the World Beneath, by Jenn. Slash, John Sheppard/Dean Winchester, John Sheppard/Rodney McKay. (ca. 67,000 words)
Stargate: Atlantis/Supernatural
This is a very cool and creepy apocafic, meshing Stargate and Supernatural in a way that makes sense for both mythologies.

Agents of Fortune, by Karasu Yurei. Gen, Dean Winchester, Sam Winchester, Alec, Lydecker, Renfro. WIP
Dark Angel/Supernatural
So far this seems to be a basic "let's make these characters meet" crossover, but it has a plot that makes sense and the way the universes are mixed is interesting. It's not exactly the canon universe for Dark Angel in that there was no Pulse, but it still feels more like a crossover than an AU premise. X5-494 is given the mission to kidnap Sam for the Manticore program, so he tries to impersonate Dean.

Bent, by Rachel Martin. Gen, Dean Winchester, Sam Winchester, Ororo Munroe, Scott Summers, Logan. (ca. 12,300 words so far) WIP
Supernatural/X-Men
This is set during the SPN episode Benders. Scott thinks that one of the Winchestes is an out-of-control mutant and goes to search for them to stop the deaths he thinks the Winchesters are responsible for.

I've accumulated enough of these to make a page worthwhile, so I've compiled all my previous crossover recs on a webpage, so that I can fix links and such in one place rather than assorted posts.

AU recs

Stargate: Atlantis

Push and its sequel Pull, by jane_elliot. Slash Rodney McKay/John Sheppard. (ca. 39,000 words and 27,000 words)
It's somewhat like a Harlequin romance story. Rodney, who works at the SGC, has an accident with Sheppard, who lives on the streets as result from his severe PTSD and dishonorable discharge, which circumstances are slowly revealed through the story. Then friendship and romance follow with a fair but not overwhelming amount of angst.

Unidentified, by the_drifter. Slash Rodney McKay/John Sheppard. (ca. 30,000 words)
Everybody recced this already, but it a really good present-day (no Stargate) amnesia AU, in which Rodney looses his memory suddenly without explanation, and we see him (re-)discovering and to some extent redefining himself and his relationships to friends and family through Sheppard's POV.

Harry Potter

The If Sieve, by Cathy (crawfords_lover). Slash, Harry/Draco. (ca. 36,000 words)
Draco goes through potential alternative universes with a pensieve-like device, exploring what would have happened if he (or Harry) made different decisions. It's a cool magical device and the scenarios are HP fandom staples, but handled in an original way, often with not quite the expected outcome.

X-Men Movieverse

Forgotten, by cyndrarae. Slash, Scott/Logan. (ca. 2,450 words)
In this AU Scott survives X3 but has amnesia, and Logan eventually finds him. Also it is hookerfic, so you get two fannish tropes in one, which in this case is definitely a good thing, since they go great together with Scott angst.

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Crossover Recs

Untitled, by siriaeve. Gen, Aiden Ford, Ronon Dex, Rodney McKay, John Sheppard, and the Endless. (ca. 750 words)
Sandman/Stargate: SG-1/Stargate: Atlantis
It's a "Five Things" type story in which SGA and SG-1 characters meet the Endless, and while each vignette is short, they are also gorgeous.