Hard to pick one for the series. I have a favourite one for each game, though.

FFI: Main Theme
FFII: Rebel Army Theme
FFIII: Eternal Wind (Famicon) or Memory of the Wind ~Legend of the Eternal Wind~ (DS)
FFIV: Prologue...
FFV: The Land Unknown
FFVI: Aria di Mezzo Caraterre
FFVII: Still More Fighting
FFVIII: Liberi Fatali
FFIX: Rose of May
FFX: To Zanarkand

I don't have the FFT and FFXII soundtracks yet, so I have not heard all the tracks in those games.