There is another soundtrack in GS: TLA that I think many forget:
Jenna's Battle Theme.
I never got around to finishing Chrono Trigger, but there is one theme in that game that I particularly enjoyed:
Frog's Theme.
There's a lot of Pok?mon game music that I like too. I won't list some of the more widely known themes like Battle! Lance/Red and such, because even though many of the older (Gen I & II) themes are very awesome, everybody knows them already.
RSE
Champion Steven Stone. The bass in Steven's encounter theme is really badass.
DPPt has some of my favorite Pok?mon tunes:
Battle! Rival. Pretty childish-sounding theme, but I think it's well made.
Battle! Team Galactic Admin. Easily my favorite from DPPt. The buildup... the breakdown... the drums... and the aftermath... it's perfect.
Battle! Dialga/Palkia.
Champion Cynthia. If it wasn't for the Team Galactic Admin battle theme being so good, this would be my favorite.
Battle! Champion Cynthia. I really like the buildup and aftermath in her theme.
Sadly, I don't have quite as many favorites when it comes to BW and BW2. But here are some:
Unwavering Emotion. I tend to prefer battle or encounter themes over all other types of themes. But I can't overlook this theme.
The Equated Captives (Encounter! N) N is so cool! :* His encounter theme is also pretty cool. And ominous.
Battle! N. His standard theme has a sense of foreboding about it. In lack of better wording. It's like noticing that your spaceship is heading toward an event horizon fast.
Decisive Battle! N. A feel of urgency. If his standard theme would describe heading toward the event horizon, this theme describes passing it.
The Pok?mon Myster Dungeon series, while not played as the traditional Pok?mon games, houses some true gems. I am thinking specifically about Explorers of Time/Darkness however, since those are the only ones I've played. I am only going to list three closely related pieces however.
Don't ever forget.... This is what truly starts the emotional roller-coaster, the ending of the main story.
Have to get home.... Your poor partner is probably still in shock from what just happened.
Farther away.... Your partner is on the rainbow stoneship. Reality hits like a freight train, your partner is starting to process the recent events.