I think Kefka had the power to destroy the entire world if he just wanted. the thing is that he is a sadistic bastard, and just enjoys terrorising the world. Who would he play around with if he killed everyone? :p
Anyway, I'm not really sure who I think is the most powerful. Zemus or Kuja would both be good choices. Zemus because he was poweful enough to manipulate a person at a great distance while still being sealed, and Kuja because he, well, could blow up an entire planet.
NOW, WITNESS THE POWER OF THIS FULLY OPERATIONAL TRANCE.