Oooh, good topic. I'll leave out the tracks from the original four PS games, as I'm sure my feelings on those are known by now.
I'll mention my favorite track from Phantasy Star Online, though. The mines boss is my favorite in the game, and the music from the second stage definitely enhances it for me, as it's my favorite music in the game:
Going waaaay back to 1997, "Catherine's Freedom" is my favorite track from the Myst soundtrack. Most of the music in those games is just supposed to be ambient, atmosphere-enhancing simple strains, but this one's got a bit more power behind it.
There are two tracks I love from Mass Effect 3, and I actually stumbled across the (free!) sheet music for them a while back. Now I can play them on my own piano whenever I want!
(Obviously these videos are not me playing. BUT I COULD!

)
I Was Lost Without You (the love theme, swooon)
An End Once and For All (no spoilers, just the music)