Yea Amity-Predator has a point, Keyes is not a villain. The dude was just doing his job and even went in to help Harrigan out. He really doesn't belong on this. Treager on the other hand is an out right dick.
And if we're going on realistic levels of evil, as far as the movies go, Burke is King. He represents everything that is evil in basic human nature.
Still the most selfish and by my definition of evil, is Elizabeth Shaw. No matter how well meaning or unintentional an evil act maybe, it is still evil and just reflects the underlining evil of human existence. Plus in the end, after all that happened in Prometheus, still took an android who she clearly should know has a ethical issue, still lets him take her to gods doorstep. Putting all of humanity in jeopardy. I mean that is the pinnacle of selfishness. Henceforth, she may not be Eric Cartman heights of evil but she is damn close to the coattails of Montgomery Burns. If we are to go with a cartoon scale here.
And that is what make a great villain. She's so villainous that most don't even notice it. She is the alien's queen.