Planescape: Torment, Persona 3, Final Fantasy VII/X, and Chrono Trigger's endings were excellent.
Fallout 1, 2, & 3 deserve special mention, however. Each one of the major character, factions, and locations has their own ending segment based on how you played them. Hearing Ron Perlman punching you in the gut after learning that your choices inadvertently doomed your favorite characters to a horrifying fate is an RPG experience I won't forget.
Clearly the best ending ever and more games could learn a thing or two from it.
You know, I've got it! The way to make FFVIII a good game!
Squall and the others say "screw you" to the clearly senile old man who raised them to be killing machines ever since they were just out of diapers. They decide they don't want to fight and kill any more and they're going to decide what to do with their lives for the first time. They then go on to form a band named Balambfish and tour the world in their floating school.
Meanwhile, in the future, since our heroes are no longer enabling her to conduct her evil plan, Ultimecia never accomplishes anything.
I'll throw my lot with Persona 3 and Chrono Trigger.
Vagrant Story had a cool ending even if it implied a sequel we never got. I also really love FFTactics' ending, in fact Matsuno has a pretty decent track record with his endings. If you count Zelda as an RPG, Twilight Princess had a really touching and beautiful ending. Of course KH 358/2 had a pretty great ending. If you want an ending that is going to just going to destroy you, that games ending comes pretty close. Lufia 2 had a really good ending. Persona2 also has some pretty good endings as well. Can't really think of any others that really stand out for me.