There are villains, and then there are villainous organizations. Usually in fiction a singular person or being is made to be the main antagonist because it's easier for people to grasp and more controlled, but a lot of the times there are also organizations that are evil which I see as really cool and closer to the real world where most of the evil you'l see will come in large numbers. So tell me your favorite ones!
Ing: This one's probably my favorite. In Metroid Prime 2 there's a planet called Aether that gets split into a light and dark half. Dark Aether holds these inter dimensional creatures called Ing that almost completely wiped out the population of Light Aether and blew up the planet by taking its energy in a war that lasted centuries. Even though the creatures seem really mindless and just like predatory beasts looking for destruction which they kind of are, but they are actually very very intelligent and war-like in their thinking. They see almost everything you do and hold a massive arsenal of creatures and such to their disposal and can possess nearly anything useful right down to robots and even corpses. It's almost a shame when they all get wiped out at the end of the game since they're so cool. They look amazing by the way here's the basic warrior from their species:
Space Pirates: Another Metroid thing which I like less than the above (in fact the ing wrecked the shit out of the pirates in Prime 2) but they're still cool. They own many planets and take whatever the hell they want and are a criminal organization so big and resilient you could explode like 3 of their home bases and they just grow stronger. To top it off their lead general is Ridley who is just cool without needing an explanation.
Combine: Sorry for taking this one but it's kind of obligatory to put in this list. I haven't even finished playing HL2 and all its parts yet but this is one cool organization that managed to own basically the planet in the course of a few years and silences anything at all that might even just slightly annoy them. And if you're going to revolt they'll know, there's a camera pointed at your face every living second of the day, so if you fight back you have to do it hard and straight-forward. As far as evil governments go in games the Combine are one of the best.