The fandoms are listed alphabetically.
Untitled Highlander AU/Andromeda, by Basingstoke. Het and slash (though there's no romantic focus, so it feels quite gen), Richie/Amanda, Duncan/Methos. (ca. 2,900 words)
These are more glimpses at a universe than a fully realized story, but the setup is just very cool.
1967 Plymouth GTX Convertible, Black., by Basingstoke. Slash, Dean/Gunn, Angel, Sam. (ca. 2,100 words)
This one is just a lot of fun. They first meet over anti-zombie supplies, there's banter, Sam and Angel are playing euchre... also Dean/Gunn!
Days Like This, by Killa. Gen, Angel, Dean Winchester. (ca. 9,200 words)
Dean and Angel meet on a hunt, and fight a gross, tentacled monster, but really the best thing in this story is the banter and the many great lines.
Stray Cat Blues, by Mary. Gen, Faith, Sam, Dean, and John Winchester. (ca. 3,500 words)
This takes place pre-series for Supernatural. The Winchesters run into Faith while on the road. (Sadly, I don't have a working link to the story anymore.)
Defect, by Kikkimax. Gen, ensemble. (ca. 39,600 words)
This is set after the second season finale of Supernatural. While Sam tries to get Dean out of the deal with the demon with the help of Bobby and Ellen, Dean is taken into custody by the FBI and interrogated and evaluated by the BAU team. I really enjoyed the take of the profiler team on Dean, and how they try to make sense of him and revise their opinions without ever actually buying into Dean's supernatural worldview.
To Conquer Fear, by Mara G. Gen, Gil Grissom, Batman and their teams. (ca. 2,800 words)
They work together to catch the Scarecrow in Las Vegas. The story is told mostly in emails and more on the fun than on the angst side of things.
Office Hours (ca. 10,000 words) and the sequel The Wisdom to Know the Difference (ca. 30,000 words), by Tartanshell. Gen, Peter Parker, Hank McCoy, Matt Murdock, and Scott Summers.
Peter meets Hank (at first not yet blue) as one of his biochemistry professors in college. This is just an awesome and very entertaining crossover, that has a great blend of humor and angst.
Agents of Fortune, by Karasu Yurei. Gen, Dean Winchester, Sam Winchester, Alec, Lydecker, Renfro. WIP
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.
Today's Tom Sawyer (1/2) and (2/2), by ladyjanelly. Gen, Sam and Ben. (ca. 5,000 words)
In 2009 Sam runs across Ben, just after the X5 children escaped from Manticore.
Hailing From Parts Unknown, by Sister Wolf. Slash, Logan (Wolverine)/Alec (X5-494). (ca. 3,500 words)
Alec and Logan and cage fights. Why wouldn't you read this?
Five Superheroes Dean Winchester Never Slept With, by Derry. Slash and het, Dean Winchester/Roy Harper, Dean Winchester/Stephanie Brown, Dean Winchester/Grace Choi, Dean Winchester/Dick Grayson, Dean Winchester/Jason Todd. (ca. 3,250 words)
The title really says it all. Dean just fits so very well into the DCU. The idea behind the Dean/Steph snippet is especially cool, but Dick and Dean bonding over their scars and Dean working with Roy were also great.
Chicago, by Carol. Gen, Carol Hathaway, Dean, Sam, John. (ca. 4,900 words)
I like outsider viewpoints, so looking at the pre-series Winchesters from Carol Hathaway's POV was really neat.
Flying Low at Night, by Cofax. Het, John Sheppard/Aeryn Sun. (ca. 8,600 words)
It's set in the same universe as Cofax's story Bellum Interruptum but I hadn't read that and still understood this story. Sheppard and Aeryn just go together like hazelnuts and chocolate as far as I'm concerned. Sheppard here is stranded in the UT, and provides a great outsider POV of Aeryn and the others.
Tomorrow and tomorrow and tomorrow, by Tassos. Gen. It's a WIP, but the parts stand well on their own. (so far three parts with ca. 36,700 words)
Crichton ends up in the Pegasus galaxy, is culled, but becomes a Runner, and finally meets the Lanteans. The first part is entirely from Crichton's POV and the story has a great way to integrate Harvey and generally show us the wackiness that's the inside of his head. Once Crichton comes to Atlantis it's just as awesome. It has great interaction between Crichton and the Lanteans.
Crooked Paths, by themonkeycabal. Gen, Rodney McKay, John Crichton, Aeryn Sun, Moya. (ca. 8,100 words)
Rodney ends up in the UTs, comes across Crichton, who is an old college rival of his, and grudgingly asks him for help to get back to Atlantis. This one is fun to read, I laughed a lot.
Untaken Roads, by Tassos. Gen, Dean Winchester, John Crichton. (ca. 4,500 words)
This gives us another glimpse at Crichton as Runner, like in the previous FS/SGA crossover by Tassos that I've also recced. And seeing him interact with Dean is just fun.
An Unlikely Meeting, by Cofax. Gen, Sam Winchester, Dean Winchester, Chiana, Rygel, John Crichton. (ca. 1,030 words)
This just a snippet, more an opening into a universe than a full story, but what we get is such a cool crossover setup that it's worth pointing out regardless.
The Monster in the Closet, by Shaye. Het, Rodney/Kaylee. (ca. 3,200 words)
Rodney and Kaylee meet as prisoners of the Reavers, so it is rather dark.
Eight Crazy Pilots Serenity Didn't Keep, by Tassos. Gen. (ca. 2,600 words)
These snippets about the Serenity crew encountering different pilots are just cool. My favorite were the ones with Luke Skywalker and John Crichton.
Riggins & Winchester, by Bone. Slash, Tim Riggins/Dean Winchester, also Billy Riggins, Sam Winchester. (ca. 4,800 words)
The Winchesters are passing through Dillon. This gives a great look at the characters, also of course it's hot.
Necessary Changes, by DevilC. Slash, Jason Street/Scott Summers, also Logan/Jean and some other pairings, both het and slash are implied. (ca. 24,000 words)
Jason discovers he's a mutant on top of everything else and is invited to attend the Xavier Institute. I'm really liking Jason here so far, and also his friendship with Tim, and of course I always have a soft spot for stories with Scott.
Clarke's Law, by Isis. Gen, ensemble, primarily Carson, Rodney, John, Hermione, Harry. (ca. 21,300 words)
The way the mythologies of HP and SGA are mixed and integrated here is just cool.
Different Kinds of Magic, by Rokeon, and its remix, by Zvi. Gen. (ca. 750 and 695 words)
Both of these are short, but still make the universes fit together great, with a cool take on John.
Old Country, by Astolat. Slash, Sam/Dean. (ca. 40,600 words)
I don't read a lot of Wincest, but I think this crossover is a great read even if you prefer gen. It's a lot of fun, humor mixed into the angst and drama, and the merge of the Potterverse with SPN here works great, and I liked the take on goblins and their magic in particular.
Winchesters at Hogwarts series, by Ignipes. Gen. (so far three stories with ca. 10,400 words)
In this crossover AU John dies and Sam and Dean are sent to wizard relatives in England, so Dean attends Hogwarts.
The Curious Incident of the Doc in the Night-time (part 2), by Taz. Gen. (ca. 2,920 words)
House meets Methos in his morgue and is understandably curious. Snark ensues.
Knight's Gambit, by Killa. Slash, Methos/Alva Keel, Duncan/Methos implied. (ca. 4,000 words)
I admit that I was a little bit lost with the demon plot in this story, because I know very little about Highlander (I've only watched a handful of the first season ages ago and a couple of xovers), but I couldn't resist the allure of Miracles fic. Even missing some of the Highlander context, this was still a very cool x-over premise, not least because Alva as an immortal would not just fit with him knowing all those languages, but explain why that investigation firm of his apparently doesn't really needs to earn money, yet he can still pay his employees.
Untitled snippet, by Pentapus. Gen. (ca. 230 words)
This is just a brief snippet, but it is a very neat idea to merge the mythologies of the two shows.
Charm City by Hth. Slash, Sam/Tim. (ca. 7,630 words)
I've only watched Homicide sporadically, but the relationships here between Sam and Dean as well as Tim and Sam really pulled me in.
New Jersey Voodoo, by Rokeon. Gen. (ca. 1,020 words)
This is short, but really funny. John has a relapse back towards Bug!John, starting with an at first innocuous rash and progressing from there, and House tries to diagnose.
Actualize This, by Helena Handbasket. Gen. (ca. 37,000 words)
Usually I dislike the "characters of different series meet at a seminar" crossover device, but this one is really funny, and well worth reading.
Verity, by Kathryn Andersen. Gen. (ca. 35,900 words)
I had some problems with the story, for example I think that Jim and Blair have a prophesied destiny in this version of the Matrix universe is overkill (one prophesied messianic figure is more than enough IMO), and wouldn't have really been necessary for the story, and I would have liked a slightly more prominent role for the Matrix characters, but overall I quite enjoyed it.
Lovers and Dreamers, by Alexia Eve. (9,472 words)
This Smallville/Muppet Show x-over, is not only hilarious, it also truly works. Lionel together with Waldorf and Statler, what more could you want?
Take Atlantis, by Siegeofangels. Gen. (ca. 800 words)
This is quite short, and doesn't really have a plot beyond "the Muppets visit Atlantis", OTOH having the Muppets on Atlantis is awesome and funny.
Take a Long Line, by Derry667. Gen, Dean Winchester, Sam Winchester, Don Eppes, Charlie Eppes, Alan Eppes. (ca. 22,000 words)
The Winchesters are trying to stop a psychic arsonist at CalSci, which we see through the eyes of the Eppes. I liked how competent Sam and Dean were in this story as well as the the outsider look at them.
The People You Meet, by Mandy's Bitch. Slash, Chris Keller/Rodney McKay. (ca. 8,300 words)
I rarely read crossovers when I just know one of the sources, but I followed a rec somewhere, and the story pulled me in. I have never actually watched any episode of Oz (so I can't judge Keller's characterization), but I think it is pre-series for Oz as well as for SGA. Anyway, it starts when Rodney gets robbed by Keller, and things get more complicated from there at a fast pace.
Untitled, by Siriaeve. Gen, Aiden Ford, Ronon Dex, Rodney McKay, John Sheppard, and the Endless. (ca. 750 words)
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.
Harvester of Eyes, by gwendolyngrace. Gen. (ca. 26,000 words)
John Winchester hunts the Corinthian, meanwhile Sam and Dean get lost in the Dreaming. This crossover is a great blend of the two sources.
Don't Mention the Wookies by Cate. Slash, McKay/Sheppard. (ca 1,400 words)
I waffled a bit whether this really counts as a real crossover, but I found its slightly wacky premise cute and funny, and it is definitely crossover-ish, so I included it in this rec set anyway.
And All the World Beneath, by Jenn. Slash, John Sheppard/Dean Winchester, John Sheppard/Rodney McKay. (ca. 67,000 words)
This is a very cool and creepy apocafic, meshing Stargate and Supernatural in a way that makes sense for both mythologies.
Untitled SGA/SPN snippets, by kitsune_tsuki WIP
So far more an enticing glimpse at a backstory and an opening snippet than a single story, but I thought the premise that Sheppard grew up as a hunter like Sam and Dean, and now encounters creepy supernatural stuff in Pegasus was cool.
Rollin', by tzi and zaganthi. Slash, Rodney McKay/Dean Winchester. (8,256 words)
This isn't a pairing or crossover that would have occurred to me, but strangely it works.
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Only Someone Running, by busaikko. Slash, Rodney McKay/Bredan Dean. (ca. 7,800 words)
This crossover has awesome plot twists, and meshes the two universes well. It is rather sad though.
Voyage par Mer, by Sealie. Gen, John, Rodney, Carson, Grant. (ca. 30,000 words)
This one is a good take on the "Rodney and Grant are related" premise. There are more parts available in her LJ here.
White Rabbit, by Valderys. Gen, John Sheppard, Grant Jansky (the author labelled it as being "pre-slash if you squint" for a bunch of pairings, but I read it as gen). (8,866 words)
This was done for the reel_sga challenge and adapts the movie Harvey. After an Ancient technology mishap John finds himself back on earth and in the past, and only Grant Jansky can see him. Donald's, Jack's and Adam's reactions to Grant seeing an invisible Air Force Colonel are great, it is a lot of fun to read.
Floodlights on the Highway, by Thassalia. Gen, Dean, Cam, Vala. (ca. 3,770 words)
How could you not enjoy Cam and Vala meeting Dean at a car show?
Nor Hell A Fury, by Lucy Gillam. Gen, Sam Winchester, Dean Winchester, Dennis Guilder, Christine. (ca. 14,800 words)
I haven't read Christine, but this was still a very enjoyable casefile type of story with neat twists in the the car's background. So if you like to read about the Winchesters hunting monsters or evil cars in this case, you should give this a try.
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On the Use of Weapons, by Cofax. Gen, Ellen Harvelle. (ca. 1,600 words)
In this snippet Ellen observes Sarah, John and Cameron at a gun show, and it gives a great outsider POV of the three.
Once Upon a Time in the West, by Marina Rusalka. Het, John Winchester/Sarah Connor. (ca. 7,660 words)
John and Sarah meet while buying weapons and ammunition. This makes for an awesome and very fitting pairing (not to mention hot), also Sam and Dean have some hilarious lines. As usual with Marina Rusalka's SPN fic the view we get of the Winchesters' pre-series family life is great, even if this is John-centric and not focused on the brothers.
Stopping for Pancakes and its sequel Looking for Salt, by dotfic. Gen, Sam Winchester, Dean Winchester, Dana Scully, Fox Mulder. (ca. 950 and 5,800 words)
If you're interested at all in Supernatural you probably have already read those two. Anyway, it's great to have Mulder and Scully interact with the Winchesters. The first takes place pre-series when Sam and Dean are still kids and Mulder and Scully are still working for the FBI, and in the second they run across each other again years later, some time during the first SPN season, and are fighting zombies together. I mean, zombies, how could you resist that? *g*
Late Nite at the Sudzy Dudz, by Sarah Ellen. Gen. (ca. 3,500 words)
I have no idea how I could have missed reading this story for so long. This crossover is a lot of fun. I guess you could sum it up as "Mulder and Scully meet the Wincesters in a laundromat and talk about cattle mutilations." but the dialog is awesome and it made me laugh a lot, while still being plausible and in character within both series.
Bent, by Rachel Martin. Gen, Dean Winchester, Sam Winchester, Ororo Munroe, Scott Summers, Logan. (ca. 12,300 words so far) WIP
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.
Case X-1743: Unresolved, by Minisinoo. Het, Mulder/Scully, Jean/Scott. (ca. 24,500 words)
While still working on the X-Files Mulder and Scully investigate the incident at Scott's high school when his powers first manifested. Years later Mulder notices Scott during Jean's tv appearance and they meet again. The plot is mostly just about getting the characters together, but I really liked how the universes meshed here.