EDIT: Oh yeah, i like the MGS3 one too! The Song is not quite as great as "the best is yet to come" from MGS1, but still pretty
Of course portal, but i also really liked the one of Devil May Cry 3.
The game ends (minor spoiler) with one of these typical "oh, there are still endless enemies to fight" scenes, and during the credits, you actually take on endless hordes of monsters.
Also, when you managed to kill a certain number of enemies, you got some bonus (i think it was a small epilogue cutscene, but not sure)
A bit silly, but fits the game.
In terms of sheer beauty, there's the ending credits of Shadow of the Colossus, even if it's a bit of a cheat since the credits start to roll before the story/game is really "over"