Hum..as I understand it, Zeromus is the physical manifestation of mankind's hatred, as explained after his defeat. Therefore, humans give him rise, giving void to the general meaning of evil, and giving no choice to the villain to exist as he is.
Sephiroth, contrary to popular belief, was nothing but a pawn of Jenova, almost oblivious to conscience. Jenova spoke through him, acted through him, but it was the real villain throughout the whole game.
Much ease for Jenova to control Sephiroth, who had been imbued by its cells.
If anyything, Professor Hojo is the most evil villain in the game, as the consequences of his study and experiments were not unknown to him, and even desired. He knew as much, as did Ptoffesor Gast who wished to seal away Jenova and keep its secret hidden.
But in the end, even beyond Hojo, Jenova was atemtping what it had to do in order to survive, that is to move from planet to planet and take all life.
Kefka was the victim of science as well, at the hands of Doctor Cid, whom unlike Hojo had no desire to create chaos, but was simply following orders from a rather dimwitted emporor.
It may easily be noticed that Kefka's situation went wrong, as Celes went through the same procedures and turned out fine. It was a whole mistake.
Who does that leave out..well, Kuja was rather evil, as upon discovering the reason for his existence, came up with the conclusion that if he cannot live, then nor should the rest of mankind. (That being based on the achievements of Kuja prior to this knowledge.)
So while being fueled by emotion, it is not as absolute as a cause of insanity, being controled or living out a part of mankind...he was the most conscious of all, therefore I suppose making him the most ''evil''..although Garland was at the hand of it all. But Kuja takes the spot for defying even his own creator for evil intent, unlike Zidane. Eh..but in the end, one may notice that Kuja never really was evil, but simply wanted a hug.
X-Death was rather evil as well, but in my opinion his motives and presence were never really fleshed out enough for a proper opinion on the subject..I suppose it leaves much for the imagination.
Well in any case, to me Kuja was the most evil villain. There are others, like Sin and Ultimecia, but I know not much of them..