Since everyone else is posting their lists, might as well toss my own two cents into the arena.
First off, clearly the finest television programs of this decade are, in no particular order, Smallville, Heroes and Battlestar Galactica. Because all had the good sense to employ, *ahem*, me. However, in the interest of objectivity, I'll leave them off the list.
Second, because I've been, well, busy the last ten years, I've missed some programming that I've heard was, well, pretty good. These MIA's include The Wire and Lost, both of which are sitting in pretty boxed DVD collections next to the television, waiting to be perused.
So here were the shows that piqued my interest in the 00's...
1) Deadwood. Easily my favorite show of the last ten years, profane and brilliant and a Western, too!
2) Sopranos. When the show was hitting the mark (which was frequently), there was nothing better on TV.
3) The Office (US version). I find the British version almost too uncomfortable to watch, but the U.S. edition manages to balance the really squirmy stuff with genuine goofball slapstick.
4) West Wing. Fast talking politics. Topical issues. Loved it.
5) 24. There have been good seasons and less good seasons, but like the Sopranos, when this show works, it's great. I'm looking forward to this season's change-up.
6) House. Sometimes I think I'll weary of House's cranky attitude, but it hasn't happened yet. This is an incredibly well written show, and Hugh Laurie somehow manages to find new angles on playing drag-addled misanthropy.
7) Law and Order C.I. Jeff Goldblum is fun, but the now departed Vincent D'Onofrio was ridiculously interesting as the obsessive Detective Goran.
8) Law and Order SVU. A little more meat and potatoes than C.I., but always well written and great performances across the board.
Honorable mentions: Bones (great chemistry between the leads), Criminal Minds (the most grisly crime show on network television!), Spectacle (Elvis Costello's interview show on the Sundance channel)...
I reserve the right to add more when my memory is jogged...