I'm trying to be objective here, as I think "best of" lists are WAY different than "favorite" lists. In terms of acting, writing, directing, and production values, these are my 10 best of the '00s. (I say this never having seen Deadwood, Six Feet Under, The Sopranos, The Wire, or The West Wing.)

Friday Night Lights
Battlestar Galactica
Buffy the Vampire Slayer
Veronica Mars
Rome
30 Rock
Arrested Development
Mad Men
Carnivale
Pushing Daisies