Off the top of my head (and I may change my mind without notice because there are way too many great Final Fantasy songs), I'd have to say the following:

FFVIII- The Landing
FFIV - Boss Battle
The Final Fantasy Prologue
FFVII - Main Theme
FFV - Clash On The Big Bridge
FFIX - Black Mage Village
FFVIII - My Mind
FFIV - Main Theme
FFV - Cursed Lands
FFVII - Oppressed People
FFX-2 - Yuna's Theme
FFX - Suteki Da Ne
FFIX - Melodies Of Life
FFVII - Those Chosen By The Planet
FFVI - Dancing Mad
FFVI - Boss Battle
FFV - Unknown Lands
FFVII - Rufus' Welcome Ceremony

And these are in the order I thought of them, not the order in which I like them. I can't say what's my favorite. And if there were any more room on the CD after that, I'd have to add J-E-N-O-V-A.