Ross from Friends...
His dorkiness killed that show, that's why he's a super evil villain!! >:O
Pretty much any villain that's not so blatantly evil is a good villain in my book.
When we tell stories, we're so stuck on "Oh the bad guy does bad things because he's bad people" side of story telling.
A Villain who is good at heart but has different intentions than the protagonists that make him bad in their eyes seems more interesting to me. I think more games/movies need more characters that are against your cause but you're still capable of liking them for who they are despite their alignment.
One of the characters in a book trilogy I want to write one day is going to be like that. Works for a group that's frowned apon for doing naughty things, but really is a character that people can relate too.. While at the same time, one of the protagonists is an anti-hero if anything, a neutral character that will help shed light on the world that they live in to the readers.
Not to sound like I'm trying to advertise anything, because at the moment my laziness has got the upper hand and chances are it will never be written LOL.
I hope that explains my ideal Villain in games/shows/movies though, since I can't think of any specifics at the moment... LOL