In a game that I played, I'd have to say General RAAM from Gears of War. RAAM is just, in my opinion, a lot more intimidating because of his monsterous size, attitude, and strength. Skorge, although he is anything from easy on the eyes himself, is just a Kantus on steroids (hence why he can jump 50ft straight up) with a chainstaff. In fact, if it wasn't for the chainstaff, Skorge would've been just an annoying Kantus with like triple health.
In a game I haven't played just watched the cutscenes online, Albert Wesker from Resident Evil 5. Everything from his hairstyle down to his voice and condesending tone, not to mention his super-human powers, just scream bad ass villian. But I like his human form better than his mutant form you fight in the last level. For some reason, a human likeness with non-human abilities is just more unsettling than seeing one of those giant, black, slug-thingys.
Oh, one more from a game I played, Dimitri Rascolov from GTA IV. He seemed like a good friend at first but then he turns on you in a very well thought out way that surprised me the first time I played the game and still does the 5th time I've played through. His cool condesending attitude along with his backstabing life-style and usually drugged out calm state from all the painkillers he takes, he's just one of those characters that you just love to hate.