Molten Core – The first end game instance. For a while this was truly the end game. The first guild that beat Ragnaros was Ascent on the Medivh server.
Blackwing Lair – Added in patch 1.6, it existed for a short time as the pinnacle of end game raiding. Drama of the Shattered Hand server was the first guild to kill Nefarian, the end boss of BWL.
Temple of Ahn'Qiraj – Added in patch 1.9, and was opened up after the server completed the opening of the gates of Ahn'Qiraj. C'Thun is the end boss of AQ 40, and was first killed by Nihilum.
Naxxramas – Released in patch 1.11. It was the final 40 man raid instance pre-bc. It had (and according to some still has) some of the most difficult encounters in game. Nihilum was the first to kill Kel'Thuzad, the final boss in Naxx.
Battle of Mount Hyjal – Released with the Burning Crusade. Nihilum claimed victory in the first world kill of Archimonde.
Black Temple – Released in patch 2.1.0. For nearly a year this was the hardest instance in the game. Nihilum claimed world firsts for every boss, including Illidan.
Sunwell Plateau – Released in patch 2.4. This will be the final raiding instance released before Wrath of the Lich King comes out. SK-Gaming claimed the world first kill of Kil'Jaden.
So all in all, Mike was close. There have been seven times the top boss in the game has changed. An argument could be made that there have only been six times, since the Black Temple was released while players were still working on Mount Hyjal; however I contend it still represents a new final boss, and thus a new top spot to be claimed.
Quite an interesting history when you think about it, especially considering Nihilum's dominance up until the final boss of the Sunwell Plateau.