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.
The classic comic book villain has severely exaggerated facial features. Also, the antogonist's head will be disproportionately larger than the rest of the body.
This is hard to describe without pictures. There have been lots of books written on this subject. Check those out or websites that have tutorial on how to draw villains.
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