For me the top of the list is Legend of Mana. I love Yoko Shimomura tunes for this one but the game per se just dragged around...
Second place goes to Parasite Eve (and Ms. Shimomura again). Never dove that deep in "Aya's adventure" although its reputation tells me to take my chances without prejudice.
Third place would be... (drums roll) Wild Arms. The complete OST is simply Michiko Naruke's greatest work. The game didn't draw me in as I thought it would...

I remember really enjoying the music in Cross Edge. I didn't hate the game or anything, but tracks like Refuse are just awesome.

Also remember enjoying Persona 1's music more than the game itself. The music for the Tesso boss fight is hilarious. A cheerful, merry carefree racket which always makes me smile.

And Lightning Returns has some pretty great tracks too. 'Death Game' and 'The Showdown' are particularly good. The game itself is okay, but the music is by far the best thing about it.

Also remember enjoying Persona 1's music more than the game itself. The music for the Tesso boss fight is hilarious. A cheerful, merry carefree racket which always makes me smile.

Yeah, this battle music is quite something. Not even future Persona composers could come up with anything like it.