Tetsuya Takahashi has great villains, I pretty much love all the bad guys from the Xeno titles. They are all pretty damn awesome and I would be hard pressed to find a series of games that can match them.

I will second Luca Blight from Suikoden II, I also really like Emperor Barabrossa from Suikoden I, and the Godwins from Suikoden V.

I love Nyalarthotep from Persona and I am really hoping the Malevolent Entity turns out to be him cause that would be awesome.

Pretty much all of Vagrant Story's antagonists are really great as well though Sydney gets special mention for being a scene stealing badass.

Wild ARMS tends to have some great villains and antagonists, largely because at first they always seem kind of generic and then the story whams you by making the situation far more complex than you think it. The Metal Demons from WA1 seem like a generic group of villains, until you start to get more backstory with them and when they begin to fight among themselves. The final boss is not going to be who you think it is. While WA2 had a... "interesting" final antagonist the meat of the plot deals with the Odessa organization, that seems like your typical "evil empire/organization" and then you get to the second disc and everything you thought you knew is turned upside down. WA3 also had an interesting revolving cast of villains as well and even a call back to WA1 with one of them.

The Sinistrals were pretty cool too, though they are fairly generic except for Iris, what made them cool was how the game really played up them being physical gods. They may not have had personality, but you certainly dreaded them showing up until you got Dual Blade.

Myria, Yuna, Fou-Lu, and the Regeants from the Breath of Fire series are all excellent protagonists. Myria is kind of a weak villain in the first game but gets some really good character development in BoFIII. Yuna is pretty much the real villain of BoFIV, but watching Fou-Lu fall from anti-hero to full villain was probably the best part of the game. The Regeants are just an awesome group of villains in BoFV and its a shame they didn't get more screen time but they were a really intriguing group of figures that makes the games world more deliciously intriguing.

The Magic Emperor from Lunar was also a great villain with a good back-story.

I will totally throw in Lavos from Chrono Trigger as well as Azala and Queen Zeal. Chrono Trigger had great villains as well.

I'll probably think of a few more eventually...