Damn, that's a tough one. Both are fine games - arguably the best of their generation. However, I'll have to give FFVI the slight edge here - I like its soundtrack a little more than CT's (*just* a little, though).

I'd also like to say that I'm also a huge fan of Secret of Mana, and if that were in the poll, I'd have an even harder time choosing. Between these and FFIV, it's hard to argue that Square wasn't at the top of their game in the early-to-mid 90's (even more so considering how limited the hardware was!)