FTL. It's the only music I have on my PC right now, for the most part, since I lost all my music a year or two back after doing a format and have been too lazy to try and find it all again. As a happy coincidence it amazes me how many games FTL's music work with and make better. I have been having it play in the background while I play games various games it it matches up so well.
Persona 3/Persona 4 (Please don't make me choose) wins it for me as far as having a bunch of awesome songs go, but if we're talking soundtrack that best fits the game it is in, I would have to say Silent Hill 2. Fits the theme and the feel of that game fantastically, but the music itself may not be as viable to listen to outside of playing the game.
Mega Man 2. Every time I hear Wily Fortress 1 or Air Man, I feel the need to play it again. It's music that still sticks in my head, randomly, on any given day. The constraints of the NES really forced composers to create songs that were astoundingly catchy, and I think they blow most modern game music out of the water. Given the aforementioned limitations and considering the time period that it was made, I have to vote for MM2.
I have to throw out FFVII to be honest. I've been replaying FFVII for the past month, just was given the keys to the Airship finally. Anyway, the game really does have solid music in my opinion.
Also a fan of the music in Jet Moto, albeit there isn't much variety.