A complex answer, depending on mood and the game I'm playing at the moment...although, if I were forced at gunpoint to select a few...
(I enjoy surreal, abstract music in addition to more mainstream ones, so depending on your own tastes these may not be particularly enjoyable)
Representative of the soundtrack's variety, although it varies from way out there to the kind of music you'd expect any large metropolitan area to produce.
Underworld theme, one of the better pieces in the game. Haunting, it goes well with the environment it plays in. The soundtrack is, like SimCity 4's, rather varied, and tend to fit the scene in which they play.
Star Ocean 2:http://www.youtube.com/watch?v=ZF080rAvxjc
"Airship" theme, one of the best the soundtrack has to offer. I, personally, don't enjoy the soundtrack as much as others, but it does have its moments.
Musashi: Samurai Legend:http://www.youtube.com/watch?v=B5Wf5rs6TLY
The ONLY good theme of the game. Very...airy. Obviously, as you're literally on a white whale of heaven that's flying through the sky.
One piece, in fact not even one that plays during the game. Yes, loading music. That's all Cybernoid 2 needs to skin open my heart and take up residence.
If I were to pick a single game that has the largest number of pieces I enjoy, Xenogears would likely get the nod. There are very few - if any - filler themes, which is rather impressive for a 70 hour game.
While I lean towards the remixes more often than not, I find that Necrofantasia cannot be easily remade into something I enjoy.
Every piece is excellent. A shame, somewhat, given that the soundtrack has only 20 some odd pieces in it. I would have preferred to link to Santa's Coming, but I could only find the Playstation port's version of the piece. Not the same.
Ys: The Oath in Felghana:http://www.youtube.com/watch?v=--kb0569o14
Imagine a rock symphony playing while fighting the hardest bosses you can imagine. Then, after barely managing to win the most epic game of Ping Pong ever conceived you realize, as I did, you're playing on Normal. There are 3 difficulties above it.
Donkey Kong Country:http://www.youtube.com/watch?v=v18pEFQb3EM
Excellent atmosphere stacked with a thick layer of butter milk pancakes. Fear Factory happens to be one of these pancakes, and so much more. Too bad the sequels didn't have scores of equal quality.
While, granted, nothing as impressive as J.E.N.O.V.A., the Atelier Iris series has memorable, fitting, down to earth music layered with a little bit of eccentricity.
Breath of Fire I-IV:
Yes, a quadruple hit of...hits. The Breath of Fire series is an oft forgotten, but long running series of classic gameplay RPGs. Being Capcom's flagship (Only?) RPG series, the music is of a high, emotive quality that's just plain fun to listen to. Perhaps the soundtracks don't match the epicness many Final Fantasy tracks do, but it would be unfair to suggest their qualities can't be compared.
One of the more underrated RPGs, Lufia II has its selection of good music. Too much filler, though. A pity.
I'm certain someone, if they went through the entire list, would be wondering where Chrono Trigger was. Here is it. Perfect game = perfect soundtrack? Perhaps.