How about Vesper? She's the perfect Bond villian in that she is never quite what she seems. Just when you think you have her figured out, she does or says something that catches you and Bond off guard. Even Bond admits he can't read her in Casino Royale. I found myself wondering throughout most of the second half of the film if she was really on Bond's side or not. When she runs off with the money, I thought I finally had her figured out to be the real villian of the film after all.... If you watch Quantum of Solace, you'll still find yourself wondering about just how "good" or "bad" she is right up to the end, even though she's dead. A character who can keep you guessing that much is a prime example of a great spy movie villian.
Some might say she's not a villian, but I say she is as she winds up hurting Bond more deeply than any of the other characters in both Casino Royale and Quantum of Solace combined.
In hero stories, its the ones who are able to strip the hero of his most important armor (that which protects his emotional heart) and wound him who are the most powerful, even if they don't look powerful at all.
Sure, Bond gets betrayed by some lovely lady in just about every movie, but Vesper violation of his trust seems to hurt him the most.