Game(s): Alpha Protocol
Agent Heck is far from your averege suit and sunglasses CIA operative. He's annoying, he's obnoxious and he's as hillarious as psychotic alleged secret agent sidekicks get. He tortures his "friend" with a bottle of cleaning solution for the location of his lost keys and fires a heavy chaingun from a speeding subway car as a "subtle distraction". There's very little doubt that Stan Smith wears Steven Heck pajamas at night. Only thing that would make him better is if we actually saw him do something like drive a 10-speed bike frame through someone's torso, like his dossier implies. Were SEGA and Obsidian savingthat for a sequel perhaps? Unfortunately, after Alpha Protocol's underwhelming sales, we'll never know.
Game(s): Starcraft, Starcraft II
Dark Templar Zeratul is like the Batman of Starcraft. His dark image makes him that much more badass and hisdabbling in the dark psionic arts has earned him a swift kick out of the Protoss society, but he would still give his life for his people just as eagerly as the bravest of the Protoss warriors. He does get accepted by his kin later on, but his dark powers never fail to make him look like the black sheep. His friendship with Jim Raynor is very fitting, with Raynor and his Raidersbeing dubbed terrorists by the Terran Dominion.
Game(s): Starfox 2, Starfox 64, Starfox Assault, Starfox Command, SSB: Brawl
Furries (and scalies ?) can indeed be badass. Wether it's his old-school aristocratic soundingself, or the more American persona from Starfox: Assault, you can see from Wolf O'Donnel's speech alone that he is one bad motherfurry. His only constant wingmate Leon is far from your averege cartoon lizard. He is supposed to be a perverted sadist, and something about himbeing a lizard does make him come off really creepy. The fact that he took on Falco during that firstbattle on the N64 makes him look even better. Despite the sheer badassery of the 2, they're not really bad guys. They don't want to take over the galaxy or anything like that. They're mercenaries - they just follow the money, not unlike StarFox.
2. Tommy Vercetti
Game(s): Grand Theft Auto: Vice City
Tommy Vercetti was the first speaking protagonist of Grand Theft Auto. Since that was a big deal on its own, Rockstar didn't seem to bother giving him a lot of depth. If you compare him to San Andreas' Carl Johnson and GTA4's Niko Bellic, the latter 2's personal lives are explored, which makes them look more human, and therefore more innocent. All we know about Tommy Vercetti on the other hand, is that he's a mobster and he recently got out of prison, making him look more villain-like, which makes him one of the most anti-heroic characters of Grand Theft Auto. Also, let's not forget the obvious influence of Scarface on Vice City.
Game(s): MGS 1-4
Who else could be on the top of this list other than Metal Gear Solid's King of Cool, Revolver Ocelot? Whether it's young Major Ocelot or the present day Shalashaska his pistol skills, slight weirdness and general awesomeness are just few of the things that had us following Hideo Kojima's saga, despite his best efforts to confuse us with his writing. If you spend some time (and tylenol) looking through Metal Gear Solid's storyline, you'll see that despite enjoying torture (and who doesn't right?), all he wants is justice. All he wants is to get back at the Patriots for playing god with his idol, Big Boss.