Final Fantasy 6. By the time I had finished that game I had come to enjoy every character in the game and the ending, especially Shadow's part, nearly had me in tears. Such a great way to end such a great game.
I liked the God of War 1 ending. You finally taking the throne as God of War is pretty sweet. God of War II set-up God of War III perfectly, with all of the Titans going towards Zeus.
God of War 2 was great. Gears 2 when you see them evacuating Jacinto. .. TR Underworld mini-level Lara;s Shadow, where you see the doppleganger get revenge on Natla at Lara's instigation.... Bioshock if you harvest a little sister before the last level you get the dark ending.
The Legend of Zelda: Ocarina of Time was awesome for the time. BioShock is best from recent memory. But I'll admit, I haven't finished some of the games that have been mentioned in this thread.
- I liked the end of Modern Warfare 1 (shooting the guy after a gun has been slid to you across the ground).. also modern warfare 2 (pulling the Knife out of you to stab the other person)
- I also love the gears of war 2 ending with the hammer of dawn from the helicopter on the lambent brumak lol