That basically sums up what's so uniquely awesome about Doctor Who crossover fic. The Doctor has a TARDIS. He can (and does) go ANYWHERE. Just For Fun. (I want one)
Windago by Rebecca Hb
Doctor Who X Avatar: The Last Airbender
Master Pakku, before he was a stuck up old man and was just a stuck up teenager, meets the Doctor and a Monster in the middle of a desolate stretch of ice. The monster is actually quite terrifying as for the first half of the story it's completely unclear exactly what this thing is and what it can do, other than the fact that at least two families have been masticated. Pakku is cold and self important, and the Doctor bounces around trying to explain water-bending with physics and telekinesis. It's everything a good Who episode is. Evil, laughter, and an awful lot of running.
Dreams and Nightmares by Anon
Doctor Who X Harry Potter
Ten and Donna meet the Marauders as they are creating the famous map. Both groups are completely surprised and confused by the others. The story focuses mostly on Remus as the thoughtful observer, which fits rather well as the story takes a nearly philosophical turn while the Doctor mad gabs about and Donna rolls her eyes at him.
The Battersea Home for Lost Robots by misswinterhill
Doctor Who X XKCD
Specifically this XKCD comic, which nearly made me cry. Seriously, Humans kind of suck. But this makes up for it. Times a million. It's short and sweet, but full of awesome.
From a World More Full of Weeping by Azar
Doctor Who X Chronicles of Narnia
Susan is one of those characters who I've looked back on with a completely different conclusion now I've "grown up" a bit. Seriuosly, her entire family dies and what I, and many other fans, came up with was "All she cares about now are boys and make-up? We don't want her in Narnia anymore". Almost to make it up to her, I've developed a special love of stories that Solve The Susan Problem. This is one of my favourites.
I Make the Glare for Lightbulbs by Voleuse
Doctor Who X Stargate:SG1
"Yes, where would we be without them?" "In the dark."
I like to imagine this as either the ninth doctor, or the fifth, shortly after regeneration. He meets Daniel Jackson in the University of Chicago Library. Both are trying to figure out who they are and what they're doing. The Doctor seems to find his way helping out Daniel, who takes this eccentric man who no longer fits his scarf with the easy stride that Daniel will later use with his adventures through the Stargate.
The Holes in the Ground by mercurial_wit
Doctor Who X Stargate Atlantis
The Doctor and Rodney McKay meet in slightly the wrong order. It's explained away by the fact that spacetime is "bendy", which Rodney finds offensive on spacetime's behalf. In the middle we see last minute rescues (by the Doctor or McKay? depends on who you ask), robot bartenders, and a reasonable dose of the prime-notprime game. When it comes full circle, spacetime is revealed to be quite bendy indeed, or funny if you get the Euclid reference.
The Man With No Name by frostfyre
Doctor Who X Firefly
Pretty long, but worth it. Desperate to find something that will help him forgive himself, or at least forget the events of Doomsday, the Doctor ends up on Persophone and hitches a ride with the Firefly crew after learning the problems of wearing a brown coat in an Alliance friendly bar. Meanwhile, Badger hires Mal to steal an alien a crime lord/honestly wealthy businessman has claimed to have discovered. Naturally, not all is as it seems, although on a second read though River's words make more sense. (Edit in bold: in my defense, it was after midnight and I'd been up since 6:30)
Portally Yours by jinxed_wood
Doctor Who X Dresden Files
Murphy meets the Doctor (who is attempting to fix an interdimensional portal in a Chicago back alley) and calls in Harry to double check that the strange British man isn't something supernaturally nasty. The characterizations in this one are pretty much dead on, which makes it even more awesome than even the concept of DresdenXWho (which is pretty sweet just on it's own) can do.