I've only seen 3 seasons, so I don't know what the full Carcetti story is yet. I'm starting to like him.
That said, my favorites are easily
Stringer Bell
Omar
Those two characters were superbly written. It was hard to hate them even though they were responsible for lots of death, despair and mayhem in the ghetto. On the other side, McNulty was another interesting character. The hero Baltimore deserves. Extremely effective at his job, but arrogant, disrespectful towards authority, and a selfish and reckless drunk drunk.
It's not too often you get stories where the two warring sides are both so rich. Take Batman The Dark Knight, for example. Bruce Wayne is a flawed hero, but you can't find anything sympathetic about the Joker. You don't even feel 'oh, poor thing, he's crazy'. He's just a bad guy that needs to be stopped. Well acted character, but not one that creates conflict in your heart.