Chances are, if the video game has a story, it's got an antagonist -- a bad guy who is trying to stop you from whatever it is you're doing. More often than not, the villain is a truly despicable person who deserves to be wiped off the face of the Earth (see: the terrorists from Counter Strike). There are a few villains, though, who aren't necessarily the worst people ever. They were pretty alright, as far as people go. Here are 4 bad guys who weren't exactly bad.
In Modern Warfare 2, one of the many subplots is that the Russians have invaded the Eastern Coast of the United States of America, and several missions involve you slaughtering lots and lots of said Russians to achieve your objectives, like recapture the White House. However, the Russians aren't invading the States just because they're evil or anything like that.
A previous mission (the controversial No Russian) shows a massacre at a Russian airport, and your character, an American undercover agent, is killed, which leads to the belief that America sponsored a terrorist attack on Russian soil. The Russian soldiers you kill aren't so bad because they think they are getting vengeance for their country.
Somewhere between the first and second Half-Life, Earth was subjugated by the alien race known as the Combine. Wallace Breen is the administrator of the whole Earth, and the foil to your heroic actions. Let's talk about how he got the job, though.
When the Combine invaded, they conquered the whole world in seven hours. This was known as the imaginatively named Seven Hour War. All of mankind would have died, if not for Breen. Breen successfully negotiated for the surrender of Earth, and humanity was not destroyed. He's the only reason there are still people on Earth. As for the Combine cruelty, Breen is powerless to stop them, as he is a figurehead for the Combine.
In Skyrim, of course there is no one story to follow. There are many different quest lines you can undertake. One of these will put you against the Empire, who have subjugated Skyrim, so you, like the good freedom fighter you are, will overthrow those pesky conquistadors!
Barring the fact that most soldiers of the Empire don't even want to be there, the Empire are really just puppets to another faction also present in Skyrim, the Thalmor. Prior to the events in Skyrim, the Empire was losing a war against the Aldmeri Dominion, so they signed the White-Gold Concordat, which rendered them pretty much powerless. One of the things outlawed by the Concordat was the worship of Talos, which is one of the main reasons the Stormcloaks (those fighting for Skyrim's independence) are rebelling in the first place. They're not wrong to rebel; they're just attacking the wrong people. The Empire has nothing to do with anything.
I'm sticking with the AC3 here, because it makes the strongest arguments for the Templars' cause. The Templars are the main rivals of the Assassins, so they engage in a clandestine war, kill each other, and somehow change the course of history. However, the Templars have noble and lofty ambitions. They want to create a perfect, peaceful world.
The Assassins feel this is somehow not a good thing, and they're not exactly wrong. Who are the Templars to decide how the world goes? However, they are the best possible people to be pulling the strings. They are simply after peace, order, and unity. Their methods may not be immaculate, but neither are those of the Assassins. Heck, their name is literally "Assassins", as in the guys who kill people. What the Templars want isn't exactly a bad thing.
These fellows all have some solid backstory and goals which make them seem less villainous in the end. Remember, not everyone you try to shoot is scum of the earth. Maybe, just maybe, they think they're right.