Note, I say 'characters', not 'villains' or 'antagonists' because for my upcoming story, the antagonist is a faceless apparition of evil. I think I liked the title they gave Ganon in Ocarina of Time: "Evil Incarnation of Darkness", too much. If the monster at the end of the tunnel is just evil, has no body, no emotions, but is a concept unto itself, it makes it easier to work with.
My characters on the other hand are half villainous themselves. They have fatal flaws that color their perception of the world. Not in a ridiculous fashion but they have anger issues, are controlling, are filled with self-doubt. They're working for money, for fame, for something they cannot tell the other characters about, because doing so would admit something about themselves they find embarrassing.
In the same way I create my villains. They have families and assets they want to protect. They want to live out their lives peacefully, even if no one else will let them. In certain situations they may be aligned with the values the heroes. People can't simply be evil for the sake of being evil. That's why so many people like the concept of fantasy races, they can be truly evil unlike a human, until you remember they have to love and reproduce like any other living creature.
My villain this year is my hero, depending on what side you're on. The eldritch abomination will attempt to foster friendship between him and people who disagree with his goal, the same people who are purposed entirely with preventing his goal from coming to fruition, but mortals have free will, something the abomination doesn't understand. The characters can make their own choice to help or hinder.
-X
