Without a doubt my personal fave would be Xenogears' very own theme of Lahan. The Creid version that is.
Suikoden 1's ending is very, very nice. Tidus' theme (piano), Vagrant Story's Staff roll, and many many more. After Cloud's spiel, I'm cutting it uber short. 😀
And is it just me, or has there NEVER been a game with a Jazz soundtrack? Mr. Bones had some nice steel stringed guitar, but as for jazz...nothing on the top of my head. Except the hair.