Hmm, well I'm going to have to concur with some people:
1. Gordon Freeman (Half Life): What can I say, not everyone is cut out to be him. He's a physics crunching badass; he's the complete package. (A cookie for that reference.)
2. Duke Nukem (Duke Nukem (duh)): Provides enough testosterone for the whole pack. Always bet on Duke.
3. Kurt Hectic (MDK): Sure he's just a janitor, but he's got a pretty cool suit and is a decent sniper. Besides, he's already saved the world twice, even if he really didn't want to.
I really wanted to be equal opportunity and have a female on the team but I figured putting a woman on any team with Duke is just asking for trouble. So I'll just come up with a ladies team. Here's my 'Charlie's Angels' version:
1. Elizabeth (Bioshock Infinite): Maybe this is cheating since the game won't be out till next year, but the woman can melt pots and pans into a molten ball of iron, with her mind!
2. Chell (Portal): This is an odd choice but every team needs a specialist. Other than the portals being handy, I figure she must have been pretty damn smart to get through Aperture. That and she can fall from any height, at any angle and land on her feet, unharmed. If the threat happen to be a murderous AI, she's got you covered.
3. Sarah Kerrigan (Starcraft): You don't get to be Queen ***** of the Universe for nothing. Hell, even before that, woe betide anybody who pisses her off.