I would have to say Omega weapon from FF5. He was a monster. I've managed to beat all the ones from the other Final Fantasies, including Omega from 8 (without The End, too). But for 5s... I even maxxed all my characters, went back, and he still wiped them out.
Honorable mentions goes to any of the last few bosses from Enix's secret dungeons (Star Ocean, Valkyrie Profile, etc). Nightmares, all of them... Star Ocean 2 had a pretty damn tough final boss... as far as final bosses are concerned. Most of them are cake. FF7s was a complete joke.