Tough one, but going with Garrus. He's just so damn awesome.
Obviously my Avatar falls pretty high up on that list too.
This is actually harder than I thought, all the characters were interesting and well written, and apart from Jacob (for his awesome combat skills, or lackthereof) I liked and used all of them pretty equally.
Garrus is still my favorite, and Tali ranks at a close second, but the others are all fightng for 3rd.