Magneto. I just love the guy. He's different from other villians. I only saw the 90's cartoon, so I don't if anything has changed, but he never really outright hated the X-men. He even worked together with them at occasions. His relationship with Xavier was one of the things I loved the most about him. They never fought unless they had a reason, otherwise they could talk "normally", and even if they had a reason, Xavier would try to talk things through with him. Not only that, but I can see why he does what he does.
I sympathize with him. In fact, I agree with him.
If you had been hated, persecuted for just being you, would you not hate the world? What if someone of great power, someone who's felt your pain, someone like you, would offer you a chance to not only get back at those who made your life hell, but also get the position of power you feel deserve, would you not take it?
TL DR: Magneto is awesome.
Oh, and if the thread was about video game villians I'll justify it by saying that there are X-men games. Therefore he counts as a video game character.