Add Payday 1 & 2 to the list. You're unequivocally bad guys doing bad things for the sake of badness (and money!), opposed by the good guys.
I guess now that I re-read your #2 and actually understand it....man, most games where you get to play someone bad dilute it by making your opponents ostensibly worse. Going through my Steam list every time I see a "bad guy" game it's set in a crap sack world where you look righteous by comparison. In that case I guess Prototype doesn't really qualify.
The Aliens vs. Predator games kind of meet this bar when you're fighting marines, but they're usually the side show to the Xenoforms.
Postal.
Syndicate kind of counts when you consider all the havoc you wreak on the civilian population. The law enforcement in that game is a little grey though IIRC, and in the game's successor Satellite Reign it's looking even greyer.
Dynasty Warriors when you play Cao Cao leading the Kingdom of Wei. He makes a lot of noise about the world needing a strong leader, yadda yadda, but you're pretty obviously the bad guy in the War of the Three Kingdoms.
Absolutely Dominions. You can play something with an evil-as-hell back story, use diabolically evil tactics and magic in gameplay and set yourself against relatively "nice" cultures and gods. I mean, you can play a god/nation where your end goal is the elimination of all life on the planet. That generally makes you the baddest of teh bad.
That Which Sleeps, although it's not technically a game yet.
Counter Strike.
Assassin's Creed: Rogue is going to be about the Templars. While that might be a shoe-in, I have no doubt it's going to go the "See, Assassin's can be dicks too!" angle. The series has always tried to make everyone look both guilty and justified, so, calling anyone the bad guy there can be difficult (when it's not bafoonishly over the top, that is. I'm looking at you, every villain in Assassin's Creed 2.)
E.Y.E Divine Cybermancy, because I dare someone to try and sort that shit out. Someone's bad though.