Before I begin, I don't like any of the typical jRPG villains. Kefka is annoying, and Sephiroth is limp. Kuja is a six foot cod piece, and Seymour is... ugh. And Fukk anyone who konsiders the kunt Ultemicia (who oddly has an unmolested C in her name.)
That said. the villains from FFXII are effective because they're actually kind of relatable, if totally fucking evil. Vayne and Cid both have a case of Ends Justify Means, with a twinge of psychosis from power. I also quite like the villains of tactics, since each of them is, in some sense or another, entertaining. They're competently written, interesting and intimidating.