Onyxia - 2 or 3 times depending on how you count, once at 60, again at ...whateveritwas, and again at 85.
Nefarian - 2
Kael'Thas - 2?
Ragnaros - once and about to be twice along with Baron Geddon, elemental lord, can't be killed, only banished yada yada
Kel'Thuzad - 2 ...and every other boss in Naxx, good point.
Anub'Arak - 2
Garr - 2
Arugal - 2
Kazzak - 2
Baron Rivendare - 2 but conspiracy theories abound, see http://www.wowpedia.org/Baron_Rivendare#Speculation
Blood Prince Council -Anyone I've missed?All of them have been fought and killed by players (Keleseth in Utgarde Keep, Valanar at Naxxanar in Borean Tundra, and Taldaram in Ahn'kahet: The Old Kingdom) and brought back to Icecrown Citadel to once again serve the Lich King.
EDITs: I guess it wasn't that bad after all, I thought there were multiple 3-timers. I personally count Ony 3 times, or else you open up the possibility of just upping any old raid instance to the new levelcap and calling it content. It was kinda nice of them to do it as a fun bit of anniversary, though, so no hard feelings. Stay mellow.