There are some appearance traits that can be used for all human comic book villains, such as a tall stature or wily smile. If the villain is non-human, red eyes or sharp teeth can be used to give it a fearsome look. Focus your villain's appearance upon both the comic's context and the personality of the villain.
Find a theme for your villain,Give your villain abilities or powers, Give your Villain weaknesses,Give the villain a personality, create a costume for your villain, and last use your imagination for the villains appearance.
If you want to learn how to draw comic book villians I would suggest getting some comic books or google image search 'comic book villians; you will be able to draw your villians using the examples you find in the books you get . another good artist to look into is roy litchentien