Oh, damn... I don't think I could ever pick just one tune as a favorite! Instead, I'll just list my top 5... er, 10, in no particular order.

"Terra"
"Cyan"
"Shadow"
"Searching for Friends"
"Dancing Mad"
"Aria di Mezzo Caraterre" (or "Darkness and Starlight" for the Black Mages' version)
"Battle to the Death"
"Under Martial Law"
"Kids Run Through the City Corner"
"Ending Theme"