the most awesome villains i can currently think of:
RE Series: Albert Wesker [this guy is badassery incarnate. he manipulated everyone. his bosses, his enemies, his bosses' rivals, his own subordinates. AND, to top it off, he could tie just about any of the ones following on this list in knots, and very likely, gut something the size of a Rex or Spino without even flinching, which gives him extra points on the badass scale
]
Batman: The Dark Knight: The Joker [Heath Ledger pulled it off FLAWLESSLY. a shame we'll never be gifted with his acting skill again
]
Half-Life Series: The G-Man [i don't need to expand on it. mysterious and capable of manipulating what seems to be EVERYTHING at the moment. he is the only guy you can find on this list that MAY be able to rival or outdo Albert Wesker...]
Sephiroth, i don't consider a real villain, so he's not on this list, though i do consider him one of my more liked characters
RE Series: N.E.M.E.S.I.S. [when you cross intelligence with muscle, size, determination, and throw a rocket launcher and a badass look into the mix, you end up with one of the most awesome monsters of modern horror. when you're walking down the streets of Racoon City in RE3 and have this guy after you, this guy's one of the few things that you actually DON'T want to meet in a dark alley...]
at a later date i'll think of who else i've seen recently and post them...