Don't we have an entire forum dedicated to this? Or is that only for Square Enix game music?

Anyway, here's some of my favorites from non SE games:

The miniboss battle music from LoZ: WW.

The music that plays during the credits of Golden Sun: The Lost Age (song 44 on the Sound Test). And most of the music from both of the Golden Sun games.

Together We Ride, from Fire Emblem (this song in varying forms has appeared in many Fire Emblem games, if I'm not mistaken. I'm going by its title in the first GBA Fire Emblem). Also most music from Fire Emblem.