I love all the FFVI songs. I think FFVI is Uematsu's best work. Perhaps that's controversial, but it's true.

There are feels and there are laughs and there are funs. Mostly a lot of feels, though. How many times have your heard someone say FFVI was the first (if not only) game that made them care about 2d sprites? The game's pathos came primarily from the music, and set the bar for everything that came after it. I can't pick a favorite but Epitaph is obviously a solid choice. I've always especially loved:

Phantom Forest
Protect the Espers!
Searching for Friends
Magitek Research Facility
The Magic House

Mostly for the way they set the tone for the zone or scene in which they were featured.