The bosses from Legend of Legaia (original)
The bosses from Einhander (one of the best games of all time) are one of the toughest you can play. (although I would not mind considering
that they look so cool blowing you away!)
And of course we cannot forget Emerald & Ruby WEAPON.
(but you can always beat them pretty easily if you combine KOTRT with Magic Plus Materia-average damage: 250,000 points.(no lie) after using that about four times, even Ruby is finished.)