Really not sure what my favourite would be. Actually, I'd have to refuse to flat out name one favourite, but I can name a few. FFIV, VII, and IX are probably around the top for me. All very strong themes as far as I'm concerned.

Surprisingly, despite my love of FFVI and it's soundtrack, I think it's battle theme is one of the weaker ones from the SNES and PSX eras. After the PSX things get a bit... weird I guess. I think X's is pretty weak, the ones that are actually in XII are great, but you don't hear them often. Didn't care for X-2's, but XIII's is actually pretty good. Certainly nothing like the older themes, but pretty good none the less.

It's also the only thing about FFXIII I didn't hate.