gannondorf (if thats how you spell it) in ocarina of time was awesome
pretty much all of the boss fights in MGS1...greatest game ever!
not sure how everyone feels about WoW but back in the day before burning crusade C'Thun was the funnest boss ever, even if he was ridiculously hard, all 40 people had to stay a certain distance apart while still being in range to attack, heal etc, then had to move around the boss together while maintaining their distance apart...took so much coordination
http://www.youtube.com/watch?v=tLAIgt6HnHY <- C'Thun kill
http://images1.wikia.nocookie.net/wowwiki/images/6/60/CThun_Positioning.jpg <- what was involved in phase one of the fight.