Since my Doctor Who obsession has led me to find several interesting crossovers, I decided to separate this list from my Big Damn List of Unusual Crossovers. Please let me know if you know about fanfics or fanart that isn't on this list, especially from fandoms that aren't represented here!

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Updated 5/3 2013: 27 crossovers

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Doctor Who

Title	Author	Crossover fandom
Comrades in Arms	waterfall8484	Anita Blake
The Eyes of the Beholder	waterfall8484	Anita Blake
Double Take	Booster	Blackpool
The Way of Things	jlrpuck	Blackpool
Watcher Who	mythichistorian	Buffy the Vampire Slayer
Guess Who’s Coming to Tea	jinxed_wood	Discworld
Near Allied	JohnAmendAll	Girl Genius
Once Upon A Time	selenak	Heroes
And Now, After All The Stars	such_heights	His Dark Materials
Fetch the Doctor, Jeeves!	idontlikegravy	Jeeves & Wooster
The Freakiest Show	yunitsa	Life On Mars
More Things in Heaven and Earth	AstroGirl	Numb3rs
A Pair of (Captain) Jacks	uktechgirl	Pirates of the Caribbean
Queer Eye for the Time Guy	Type 40	Queer Eye for the Straight Guy
Seems Far From Home, Seems Farther From You	fryadvocate	Stargate Atlantis
Crackaboom	Kesomon	Stargate SG-1
Gate of Orion	Kesomon	Stargate SG-1
Goddesses, Consorts, and Explosions	ladyyueh	Stargate SG-1
Military Intelligence	nostalgia_lj	Stargate SG-1
Crashing Chandeliers (The Teachers and Students Remix)	amaresu	St Trinian's
Two to Make Peace	Kathryn Andersen	The Vorkosigan Saga

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Torchwood

Title	Author	Crossover fandom
A few quiet drinks	jadesfire2808	Discworld
First "Six Degrees" meme ficlet	selenak	Heroes
Vinegar Pistol	puritybrown	Scrubs
Can't Trace Time	legionseagle	The Vorkosigan Saga

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Doctor Who and Torchwood

Title	Author	Crossover fandom
Past Improbable	sixth_light	Bones
Club Night	jadesfire2808	Discworld