I loved the endings to Metal Gear Solid and Metal Gear Solid 2. Kojima has this way of building things up, and then blowing you away at the end (or leaving you confused? lol) The original Metal Gear Solid was so unique; just when you thought you beat Liquid and the game is over, you still have to escape Shadow Moses before it gets nuked. This leads to a high speed chase where Liquid comes back out of no where, and you have to shoot the crap out of everyone before time runs out. Then the games ends with a couple revelations, and the characters talking about life and what's next. The credits play with some of the best music I ever heard. And then when you thought it was truly over, the game ends with yet another plot reveal, via codec. It sets you up for the next game nicely. As for Metal Gear Solid 2's ending, it's kind of like 1's ending, but on on some serious far out their drugs, lol. But I love it anyway.
What about you, SW? What game(s) have the best ending?