Dark Messenger (Whoever doesn't know when this plays, well, shame on you)
Bran Bal, The Village Without Souls (Dark music that plays as you arrive in Terra)
The Final Battle (Yes it does sound kind of odd, but the tune really fits the theme of danger)
The Place I'll Return To Someday (As well as the 'darker' remix that plays in Oeilvert. I just love those types in general)
Crossing Those Hills (Field Theme Music I think)
Mystery Sword (Music that plays in the Beatrix battles)
Loss of Me (When Beatrix goes all emo on the Red Rose)
You're Not Alone (When Zidane 'malfunctions' in Pandemonium)

These are among my favorites, but I'd have to go with The Final Battle as my main favorite, with Dark Messenger in second.