Emperor Mateus in Final Fantasy II. When you finally face the Big Bad on his throne room, the boss fight is depressingly easy. A good party ends up killing him rather quickly. Then the Dark Knight steps forward, and you think that the Emperor was a Trick Boss, and that Dark Knight was the Man Behind the Man. But then the Emperor reappears on his throne, in a new monstrous form. Turns out that he died and went to Hell... and then took it over!
Then, of course, the party scores a collective moment when the literally go to Hell and back to beat the Emperor.
In the GBA and PSP remake, all the dead party members go to Heaven, and beat the light half of the Emperor! (Yup, the Emperor is so bad that even his GOOD side was evil!)
Also, Minwu getting Ultima, period. The one dedicated White Mage in the game finally gaining access to the ultimate White Magic? That he sacrificed his life to unseal for the heroes? And surviving (well, sort of...) unsealing it a second time before having to battle freakin' Ultima Weapon to prove his worthiness to wield it? Suffice to say, there's a reason he's an Ensemble Darkhorse (and being able to use it on the Light Emperor can be an epic moment of player catharsis).
When Josef sacrifices himself so that the rest of the party can escape after defeating Borghen.
The opening FMV from the Origins remake deserves a mention.