Funny you should mention this, I actually did an essay on this a while back, and the answer is green and purple.
This is because original heroes traditionally wore bright primary colours such as red, blue, and yellow (think of Superman), and so to help readers understand who the main villain was, writers would illustrate their villains wearing the colours opposite to the heroes; secondary colours, usually only green and purple.
Think of the Joker, Lex Luthor, Green Goblin, etc. Even though Batman doesn't wear the hero colours, Joker still wears villain colours.
So to answer your question, green and purple.