I'm surprised nobodies mentioned Conrad Verner yet. He's just laughably pathetic but turns out not to be so bad of a guy once you figure him out. Plus he's a gaming "number one fan" character done right. A little bit of stalker, a little bit of cockiness, and a plethora of excuses and lack of intelligence. Not only that but after the first game he breaks the 4th wall like there's no tomorrow by openly mocking developers and players alike.
As far as squadmates I always liked Jack. She set up these layers of defenses to keep the world away and all of them can be peeled away by your Shepard. Her role and re-design in the 3rd one were both awesome and appropriate.