I feel like a dirty, dirty fanboy saying this, but I'd nominate Final Fantasy III/VI/Whatever for an honorable mention. I would love to see the ending of that game on current gen technology with a truly symphonic score, as it neatly closed out the game. Not the game, mind you; I've lost interest in the JRPG genre but will always have a soft spot for that one.
Bioshock's 'good' ending was touching, but perhaps a little bit of a sucker punch and certainly not that effective when the protagonist is a faceless stand-in for the player. Frankly, he has the personality of a broom.
Halo 3? I've found every aspect of the Halo series overrated, the ending no exception. No part of Halo was bad, and most were good, but it most certainly isn't the great FPS savior to which all other FPSes should be compared. Still, the finale of Halo 3 was good, though predictable.
I'm going to go on a limb and say Torment. The idea of the Nameless One owning up to his endless sins, accepting damnation, with Grace swearing to seek him through all the hells before her rushes off to his punishment? Yeah...
And I found Deus Ex (and DX: Invisible War) strangely compelling in their dystopian visions for each ending.