1) Omar Little on The Wire: The closest The Wire ever came to a larger than life character, but he was just human enough to feel real and apparently the real Omar did some even cooler stuff. He was frank about his homosexuality, the scariest gun-slinger in the 'hood and hates swearing. Funny too! What's not to love?
2) Veronica Mars on, uh, Veronica Mars: It was either her or Hank from Terriers and Ms. Mars had more time to be fleshed out. Funny, tough, and soulful, Veronica Mars was a great 21st century P.I.
3) Walter White on Breaking Bad: Breaking Bad was fearless in the fact that they took Walter White from an anti-hero (His intentions were good, after all) to a flat-out sociopathic villain with a pretty high body count who has hurt a lot of others, including children. Obsessed with building an empire on a truly insidious drug. I can talk about the characterization of Walt for hours. Tony Soprano could also fill this slot, but The Sopranos debuted in 1999.
4) Doctor Perry Cox on Scrubs: Scrubs had a lot of great characters and my second favorite was Turk, but the real heart of the show was John C. McGinley as Perry Cox, the gruff, suffers no fools, hard-working doctor and father, Always ready with a rant or an insult, or a tough lesson, he was just a great character. A crime he never got an Emmy
5) Michael Bluth on Arrested Development: Because he was smarter than the rest of his family and truly cared for his son, it's kind of surprising when you realize that he's just as bad as the rest of them (His treatment of George Michael's perfectly nice girlfriend, Anne, for example). A great straight man to the chaos around him. He grounded the show, even when I didn't care for it. (A good chunk of season 3 and when characters like his brother Tobias got too cartoony)
6) Vic Mackie on The Shield: A true noir anti-hero, the best James Ellroy protagonist that he never wrote. Arrogant, charismatic, a bully and psychopath. Every good deed he does has a second darker subtext. A true predator and king of his urban jungle. His actions destroyed so many people. The other most interesting protagonist of the 21st besides Walter White.
7) Charlie Crews on Life: I loved the cop drama Life and Damian Lewis as the cop turned convict turned zen following cop was the reason why. He was fascinating, always talking about peace and finding your center while bubbling over with rage and thinking like a hardened ex-con (one of the best things the show did was hint at the truly dark shit done to and by Crews in prison, but never showed it)
8) Barney Stinson on How I Met Your Mother: Probably my favorite traditional sitcom character ever. Barney is the typical horn-dog every show seems to have, but NPH and the writers add some real pathos to him as it's shown that he's actually a pretty damaged guy. His road from cartoon to real boy headed for marriage is completely believable.
9) Boyd Crowder on Justified: Probably my favorite anti-hero on TV. You never know what side he's on and the angle he's playing. Plus, he chews scenery like nobody's business and is entertaining about it rather than obnoxious.
10) Coach Eric Taylor on Friday Night Lights: FNL was a great show and Kyle Chandler's Eric Taylor was a big reason why as one half of the best marriage on TV. He was everyone's friend, a true man, a father figure and a MOLDER OF MEN, as his wife once said.