I don't really know... It's hard to pick just one. They're all so good.
I suppose it depends on which one you think fits the mood best. For most emotional? The Last Day of the World hands down. Most dramatic? Lavos's Theme, probably. Best battle music? Well, either World Revolution or The Last Battle, of course. :p I like Battle 2 for some reason though. Best area BGM? Singing Mountain, of course. ;) I love the soft, peaceful, melodious tune. Chrono Trigger is a pretty good theme too, as are the PC themes. (And Schala's too. :D)
Like I said, it's hard to pick just one. They're all excellent in different ways.
(One thing I have to say, though, is that every single theme in the Chrono series is not a song. Pieces of music are only songs if they have lyrics. Otherwise, they're themes or musics)