Game: Half-Life
What Makes Him Bad: Signing over the Earth to the Combine in return for becoming the "ruler" of the planet. More like a figurehead, actually.
What Makes Him Cool: Dr. Breen looks like a mega-goof when you play around with his character model in G-Mod.

Dr. Breen signed the Earth away in exchange for safety and a peaceful pact that essentially made him the ruler of the entire planet, even if that meant just making him a figurehead. And you need an explanation as to what makes him a bad guy? Contemplate that for a moment. All of us. Signed us away. To the Combine.