Breath of Fire 2 - The final boss.
St. Evans (Jesus) turns you and all of your party to crystals, but you break out. He paralyzes you and shatters your friends. Proceed with one of the most awesome sequences ever in a SNES RPG.
Xenogears - Bart and the Yggsdrasil versus Id.
You threw a ship at me. Take it back.
Persona 2 Innocent Sin - Some of the more exotic and absurd rumors.
Hitler was a boss.
Wild Arms - Ziekfried's Last stand.
"I shall take you with me!" *grabs Rudy's arm and Rudy tries to cut the binding with his sword* "Fool! No human weapon could cut that!" *Rudy cuts off his arm.*
The Final Fantasy Legend - The final boss.
You fight God, who incidentally has a bitching hat.
Persona 4 - True Ending. Major Spoilers.
This.