I think the best villain apart from Sephiroth is Beatrix, when she was a villain.
Okay, okay, she became a good guy later, but when she was a villain, she was kick-ass. She is just so smooth and cool about everything. Including kickin' your party's ass!
Another great villain was Heidegger, gnah, gnah. What a fat bastard! With his stupid laugh. But a very evil laugh! Gnah, gnah.....(who laughs like that?)
And don't forget Gilgamesh from Final Fantasy V, this dude had his own theme. He was this stumbling retard, who just kept getting stronger and stronger. But in the end, he showed he wasn't THAT big of a retard, which made him utterly cool!