The Castlevania series has a lot of fantastic music, especially Symphony of the Night.
And while I've come to mostly dislike the Megaman series, I do enjoy pretty much all its music.
I actually like most of the tyrant themes for Resident Evil games, especially "The 2nd Malformation of G" from RE2.
Cobra mentioned that he likes Donkey Kong Country's water music tracks; I'd have to agree with you there. My particular favorite is DKC 3's water theme.
I guess I don't have a specific track I could proclaim is greatest. My taste shifts around too much.
And I have way too many favorites, usually a handful from each game's sountrack. To list them all would be inane.

For those who need access --
http://gh.ffshrine.org/Best site for amassing your faves.
Also, I'm surprised someone hasn't yet brought up Final Fantasy VII's One-Winged Angel as their all time favorite.
'cause really... at any given point in time, someone is raving about this damn track.