I like villains (and heroes) who have insecurities. Especially villains who are driven (in whole or in part) by their insecurities. Also, villains who have an interesting relationship with their underlings.

I think several of my favorite villains have similar motives to their heroes.  They both want the same or similar things, but there's some difference in how they go about getting it or what they do with it that sets them apart.  But I really dig the concept of doppelganger, be they strictly evil clones or the more general less photocopy-like sense--being able to defeat a version of yourself is a concept that really grabs my attention--so I don't know if that's a direction you want to take things in or not.

I suppose I'm also used to villains with overwhelming powers who are difficult to stand up to, and even when you can stop them they prove exceptionally resilient.  But that runs a serious risk of pulling in deus ex machina and such, so I'd say exercise caution on that front.

I like villains who think they're in the right.

Not mass murderers or insane people, villains who think what they are fighting for is right, even if it isn't.

Sorta like Archie and Maxie from Pokemon. They think they're helping but they aren't.

Traferous. Teridax. Captain Kirk. Roodaka. Captain Tromeneg. Ghidora.

Cap'n Kirk was a villain?  ...  I need to learn me some Starm Track.

Traferous. Teridax. Captain Kirk. Roodaka. Captain Tromeneg. Ghidora.

The Sinister Seven - you missed Sam Sinister.

Cap'n Kirk was a villain?  ...  I need to learn me some Starm Track.

>villain

>totally a villain

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(no seriously, he wasn't one, but all good villains share at least some qualities with old James T.)