1. Sephiroth
2. Kuja
3. Kefka
Top 3 were very close together, no other main villain came even close to invoking the scene of danger that these three did.
4. Golbez
Despite not being a main villain, Golbez makes a good attempt, the music the feats, character death (or at least departures from your crew whenever he showed up) he had you running.
5. Edea
Yes Edea, seducing Seifer to her side, mindcontrolling Rinoa, thrusting an icepick into Squalls chest whn he confronted her, she had *****ing scenes.

In my mind nobody comes close to these five.