Rat Creature's Journal

Pass the Pork-Barrel Salt, by Gwendolyn Grace and Etakyma. Gen, Sam Winchester, Dean Winchester, Josh Lyman, Donna Moss, C.J. Cregg. (ca. 5,000 words)
Supernatural/The West Wing
Josh meets the Winchesters during a "Big Block of Cheese Day". This crossover is simply a lot of fun.

Begotten and Gingerbread, by Nilchance. Gen, Alec, Sam Winchester, Dean Winchester, Boby Singer. WIP
Dark Angel/Supernatural
I'm not actually sure whether this is a series or a WIP, but I find it intriguing so far, because in this crossover the timelines of DA and SPN don't seem to have been messed with to mesh them, but instead Alec somehow ended up in 2008, though neither he nor the Winchesters seem to know the how or why yet.

Travelled on his looks, by Petronelle. Gen, Fraser, Ray K., Dick Grayson, Tim Drake. (ca. 2,200 words)
DC Universe/Due South
I'm not much interested in crossdressing, but Fraser and Ray teaming up with the Batclan here was fun.

Untitled, by Tassosss. Gen, Teyla Emmagan, Aeryn Sun. (ca. 2,840 words)
Farscape/Stargate: Atlantis
Teyla and Aeryn team up for a jailbreak, which is simply a great scenario.

Woman Inflammable, by Vehemently. Gen, John Winchester, Sarah Connor. (ca. 4,660 words)
Supernatural/Terminator: The Sarah Connor Chronicles
I really enjoyed this insight into John at the beginning of his hunting life, and the outsider look at Sarah. And of course John would have the worst luck in that that he picks Sarah Connor & Co to run into early on.

where the grass is green and the girls are pretty (ca. 2,165 words) and its sequel oh, won't you please take me home (ca. 2,700 words), by Vorrothiel. Gen, Ash, John Connor.
Supernatural/Terminator
There's something about crossovers between Supernatural and Terminator that really appeals to me. The universes just go together like hazelnuts and chocolate, IMO. Anyway, this one has the unique premise that Ash used to know John Connor in high school.

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.

AUs

Dearest, by Lavvyan. Slash, John Sheppard/Rodney McKay. (ca. 4,200 words)
The people with the ATA gene are regarded as pets in this AU, though then it turned somewhat atypical for slave/mindcontrol fic (and has a sad ending), but it still worked for my kinks.

After Such Knowledge, by Sarah T. Het, Michael/Teyla Emmagan. (ca. 7,500 words)
This is an AU of Michael's storyline, with the premise that Michael chose to remain human because Teyla was more honest with him.

Sequelae, by The Spike. Gen, John Sheppard, Rodney McKay, Jennifer Keller. (ca. 26,000 words)
It's a futurefic that goes AU during Adrift, though the past of how Atlantis was lost and the cause of the rift in John and Rodney's friendship is only gradually revealed, as John suddenly shows up at Rodney's doorstep, having a retrovirus relapse.

Pegasus Ascendant, by Tielan. Gen, Teyla Emmagan. (ca. 1,830 words)
Pegasus is without Wraith and various Pegasus people share control over Atlantis as the Earth expedition makes contact. I find the premise here very cool, though I wished there was more than this opening. I'm definitely hoping for a sequel.

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crossovers

Only Someone Running, by busaikko. Slash, Rodney McKay/Brendan Dean. (ca. 7,800 words)
Stargate: Atlantis/Thoughtcrimes
This crossover has awesome plot twists, and meshes the two universes well. It is rather sad though.

On the Use of Weapons, by Cofax. Gen, Ellen Harvelle. (ca. 1,600 words)
Supernatural/Terminator: The Sarah Connor Chronicles
In this snippet Ellen observes Sarah, John and Cameron at a gun show, and it gives a great outsider POV of the three.

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Also when I asked on the SGA genrefinder comm for stories with Sheppard as an Ancient or Sheppard ascending, I compiled a list of stories in that genre I had already come across, so I thought I might just as well repost that list on my website as reference. Here's a link collection with stories featuring John Sheppard as Ancient, Ori or Ascended. If you come across any I missed, let me know.

I'm still reading SGA holiday exchange stories and have also started browsing the now live Yuletide archive, so here's a couple of recs:

SGA

Red Flowers, by Anonymous. Teamfic. (ca 25,620 words)
This is a great action-adventure teamfic with cool world building of a Pegasus civilization. It has some Sheppard/McKay as established background pairing, but that is minor and the focus is on the whole team with Teyla and Ronon playing nearly equal parts to Rodney and John, though it is slightly Rodney-centric overall. So unless you hate the pairing like the plague, you'll enjoy it as a plotty team story with aliens, Pegasus politics, just the right amount of technobabble and explosions, even if the listed pairing isn't your thing.

Dresden Files (bookverse)

The World's Largest Kitten, by Anonymous. (ca. 1,200 words)
This is just really cute and fun fluff with Mister and Mouse.

Terminator

How to Change the World Without Even Trying, by Anonymous. (ca. 1,400 words)
It's a characterstudy looking at John, and how the world his mother raised him in is removed from the mainstream, and then John's view of his foster families and his changing perspective on his mother.