My top ten has a few unheard of songs, but here it is:
#10: Earthbound: Pokey Means Business
#9 Xenogears: The One Who is Torn Apart/One Who Bares Fangs at God
#8 Zelda, Skyward Sword: Zelda's Lullaby
#7 Arc Rise Fantasia: In Order to Understand my Fate (Underrated game!)
#6 The World Ends with You: Run Away
#5 Chrono Cross: The Girl who Stole the Stars
#4 Zelda, Wind Waker: Helmaroc King
#3 LoH: Trails in the Sky: Silver Will
#2 Xenoblade: Satorl Marsh (Night)
#1 Ys Seven: Disappearance of Reason
Estelle and Adol... best characters ever! XD