For me there is no doubt it will have to be:

{drum rolls}

Metal Gear Solid 3

AND

Final Fantasy X

So what are yours?? Please have a link if possible

MGS 3



_______________________
FFX

the Nod ending for Command & Conquer 95, which can be seen here -

http://youtube.com/watch?v=4b05hLEZwBA

Edit - fixed link 

@spire_VII

it doesn't work!

^^I cried like a baby at the Kingdom Hearts ending (especially since I didn't know there would be sequels yet)

Wow, talk about the single best way to reveal as many spoilers as possible.

Please just say the ending of the game, and if you have to, black out the spoilers. You just told me the end of a game I've never played, and although I never intend to, I'm annoyed now.

Anywho, I think the ending of Grand Theft Auto: San Andreas was perfect. It fit the game so well.

@Montana Hatchet

sorry I didn't know how to block out spoilers..

Final Fantasy VII or Sonic the Hedgehog 2

(or even the ending for every atari 2600 game, rolling color screen makes me weep)

I think the ending of Legend of Zelda: Ocarina of Time.
The neverending different fight models of the final boss. The destruction of the big castle while trying to exit it. The unexpected last confrontation of the supposedly beaten boss. The 20 minute ending festive parade with all the characters and the dynamic 10 minute midi orchestration of the most memorable in-game tunes.