There are plenty to choose from in this Bioware Epic. Is it the solarian scientist Mordin? The psycho prison inmate Jack? The genetically enhanced Krogan Grunt? The bad ass Garrus? One of the many other characters offered in this instant classic?
They are all very valid choices because Bioware did such an amazing job fleshing out all these characters with deep dialog trees and emotional loyalty missions. However my favorite is far and away the downloadable content character Kasumi, she is some sort of awesome ninja thief that also unlocks a beastly sub machine gun. Her special move is teleporting behind the enemy and then delivering a fatal smack to the back of the head.. Pretty cool if you ask me.
I'm sure its safe to say that Commander Shepard himself is the number one contender for everyone's favorite. In Mass Effect 2 he's actually cooler than he was than the last time.