Hope's theme, in both Final Fantasy XIII and it's sequel. His theme's to me felt slow and calm, and sort of defined his character. Sustained by Hate is one of my top ten tracks in Final Fantasy XIII, and it showed the plight of not only him but all of the main characters.
Runner up is Auron's theme. It's badass, need I say more?
For the villains, I would say Golbez's from FFIV. Every time Golbez's theme popped up when I first played the game, I knew something bad was about to happen. (And it normally does)