Final Fantasy VI had so many amazing bosses. Atmaweapon was so exhilarating with its size and the music that kicked in. Fighting to the top of the tower and watching Kefka descend from the heavens was amzing as well.
Still, watching Necrosaro evolve during the battle after experiencing his story with the elf girl (Rosa?) in Dragon Warrior IV was the first time an RPG took my breath away. It was also the first time I ever saw an enemy move in battl, so I was suitably impressed.
Luca Blight is still probably the coolest, though, just due to the fact that it takes an army to weaken him enough that you can duel him and he even fights you after being shot full of arrows.
Of course, Indalecio in Star Ocean 2 took me days to kill (I eventually got some bunny shoes which made it easier, but not easy).
Killing Deus in Xenogears is pretty awesome too, since you can either kill his angels first, or take everything on at once.
Suikoden III's final boss was awesome just because of who it was.
Fighting the Tyrannasuarus Rex in Parasite Eve was quite a fond memory as well.