Sayid/Jack ; Sayid/Charlie ; Jack/Sawyer - Lost
House/Cameron ; House/Wilson ; House/almost anybody - House, M.D.
Remus/Sirius ; Harry/Hermione (cuz I saw the movie first and thought dan and emma had better chemistry) ; Hermione/George (my fav. twin) ; Harry/Cedric - HP
Matt/Mohinder ; Peter/Mohinder ; Mohinder/almost anybody - Heroes
Drake/Josh (yes I know it's a nick show but...have you ever watched it??)
Tumnus/Lucy (stop your groaning...a well written story can be cute) - Narnia
Boromir, Legolas, Faramir, Aragorn mixed up in many different ways. - LOTR
I'm sure there are others I'm forgetting, but that's enough for now. :-)