This is going to be tough, but here are mine, in no particular order. I also will try to avoid spoilers if I have any spoilers come from scenes with the music.
Single game - Astal:
The Crystal Palace. Astal actually has some pretty great music, but this one sticks out to me the most. It's a calm yet amazing track, plus the fact that it's close to the end of the game makes it have a bit of an uplifting effect.
Atelier series - Mana Khemia:
Nefertiti. This is just a really great boss battle theme, in fact, I found it hard to choose between a lot of music from the game. This is one of the themes that most people consider the best, so I chose it. There's no real deep meaning from it for me, it's just an awesome battle theme.
Final Fantasy series - Final Fantasy IX:
You're Not Alone!. This was even harder, I had to choose between two XI tracks and another from IX. I picked this one because I know the XI tracks may wind up being posted anyway. Also, this one is actually one of my favourite things of music to listen to because of how oddly uplifting and powerful it feels.
Disgaea series(Makai series? Not sure.) - Phantom Brave:
Heaven's Garden. (Warning: Vocals) This was another hard choice, Disgaea 2's credits being the other one. But this song really just seems like everything in the game combined into one. There's not really that much I can say about it other than the way it's used in the game works in a way that makes me love it more.
MOTHER/Earthbound series - MOTHER 3:
It Is Finished. This, just this. This is what most people who have played MOTHER 3 heard as they realized there was water coming from their eyes and running down their cheeks. In fact, I beat the game 2 years ago and I still tear up just from this. I also wind up getting chills from most of the tracks in the entire series. It's probably the most emotional track in a game I've ever heard, next to the Love Theme, which this essentially is, I just chose this version because of what's going on when it plays.
Well, that was the hardest list I've put together and I'll take this time to say that I recommend the music from each of those games and series, not just the songs I posted, they're all great.