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Whoniverse:

Doctor/Jack. SO MUCH.
Jack/Martha. (Well, at least she's A doctor. Heh.)
Tosh/Owen. (RIP. x2.)

BSG:

Adama/Roslin. Asides from it being practically canon... well, they're just awesome.
Helo/Athena. Canon. Also, awesome.
Baltar/Caprica(/Head!Six).... does there need to be a reason?

Whedonverse:

Cordelia/Angel.
Faith/Robin.
WILLOW/TARA. *sobs*
Xander/Anya.
Giles/Jenny. *sniff*
Dawn/Connor (don't ask me why. Really, don't.)

Simon/Kaylee (though Jayne/Kaylee is an acceptable alternative)
Wash/Zoe
Mal/Inara