Out of the villains of the games I've played, Sephiroth definitely seems to be the most powerful.

Although I was always partial to Shinra from FF X-2 (which is why he's my avatar). For some reason he just seems incredibly powerful. And that's besides the fact that he can casually kill any enemy in the game without too much trouble, except for himself. And Trema's gonna take a long time, but other than that nothing can stop him.

Not to mention he was created by Shinra filling in as the "king of the underworld". Finally, his signature attack, "Clione", is awesome. One hell of a superboss.