I can't make up my mind about this, so here's a list of good themes:

Sephiroth's theme
Aeris' theme
Terra's/Tina's theme
Shadow's theme
Auron's theme
Seymore's theme (there was an undercurrent of madness in it, an' that's ace)

Freya's theme would make it onto the list with a different instrumentation (I think it sounds, well, sissified - if you must dispute this, use PM). Also, I didn't include OWA because it's a battle, the topic demanded a theme. Same reason for not including Anxious Heart, among others.