Originally, these were two separate lists, but there was too much overlap; there are five stories on here that belong clearly on one or the other, but all thes rest fit both. Whatever, awesome cliches that have the bonus of being canon in several of these fandoms.
Anyway. Standard warnings for this type of thing: Worlds where everybody's dead/everything's gone horribly wrong! Worlds where everybody's a different gender! Worlds where everything could have been so much better if only you'd been smarter/braver/less crazy, you joykilling bastard! So-and-so has sex with their alternate self/clone/past self!
Oh, and also some noncon, incest in Dabarim, and bonus surprise sort-of incest in another story, but it's hilarious and a warning would spoil it. If you desperately need to know, comment and ask.
01.
Anything you can do... (Harry/Tonks) [Harry Potter]
02.
Dabarim (Sam/Dean) [Supernatural]
03.
Famous People You Can Live Through (Justin/JC) [Popslash]
04.
Desperate Measures (Harry/Harry, Harry/Draco) [Harry Potter]
05.
A Gift of Ordinary Magic (gen) [BtVS/Harry Potter]
06.
This fever, spreading (Batman/Flash) [DCU]
07.
Earthbound Spook (Harry/Draco) [Harry Potter]
08.
Promised Eternity (A Ring of Endless Light Remix) (Remus/Sirius) [Harry Potter]
09.
Make My Troubles Rhyme (Pete Wentz/Patrick Stump) [RPS]
10.
Worlds Together (Various) [Harry Potter]
11.
A Black Comedy (Various) [Harry Potter] (WiP)
12.
Normalize (John/Rodney) [Stargate Atlantis]
13.
Taking the Long Way Home (sequels/companions
here) (John/Rodney) [Stargate Atlantis]
14.
Water Hold Me Down (part of the
Whisperverse) (Xander/Faith, Xander/Anya) [BtVS] (WiP)
15.
Journey to Another Hell (Xander/Jean Claude/Asher, Xander/Nathaniel) [BtVS/Anita Blake] (Series Incomplete)