It wasn't an especially "great" boss fight, but beating the final boss of Star Ocean 2 was the most difficult fight I'd gone through in an RPG. I was only at level 103 or so, which may have been lower than I should have been, but, damn, he was hard. You had to constantly attack him, and he could move around like crazy, and if you let him transform you were screwed--problem was, he could sometimes transform even when you were pummeling him, so it took a lot of luck and speed to kill him. I fought that guy so many times. xD

The battle with the Hydra in God of War was pretty awesome, but the final showdown with Ganon in OOT was probably my favorite.