There's a significant limitation to these amateur lists---what about the ones we just didn't see? I've never seen Big Love, The Wire or Dexter Season Three, for instance. Wasn't John Adams a 2007 series, which is why it did so well at the 2008 Emmies?
In no particular order, as I couldn't assign numerical values without a checklist I didn't feel like writing---
Pushing Daisies (ABC) Either you get past the pastels or you don't. Unique.
Breaking Bad (AMC) "Dark and gritty" and "moral ambiguity" is usually just posturing. Already close to lapsing into glorification of evil but the first season is astounding. The pilot was the worst episode!
Lost (ABC) Really, the series storyline is hopeless. But this show is so inventive! Almost all nonsense on TV is tiresomely drab. This breaks the mold.
CSI (CBS) The real one, not the wretched spinoffs. Notable for its wide variety in episodes. Anybody who babbles about cookie cutter is style deaf.
Numb3rs (CBS) Solid character work---the Eppes brothers are completely different, except they're alike. That's real people. Plus math!
The Closer (TNT) Kyra Sedgwick sells a lying, terminally tight assed bitch as someone whose commitment to the law saves her from being one of the bad guys.
Brothers & Sisters (ABC) Nothing will top the first year but by far the best nighttime soap. Hysterically funny without being a farce, something most comedies can't manage.
ER (NBC) The soap part is a little tired, but they still do medical drama with some real medicine and real drama.
30 Rock (NBC) Alec Baldwin, Tracy Morgan and Tina Fey. My sides hurt.
Scrubs (NBC) The serialization of comedy has reached diminishing returns but the bottom of this series is higher than most comedies ever reach.
Burn Notice (USA) The light touch at its deftest. Michael's relationships have sentiment without sentimentality.
Big Bang Theory (CBS) Chuck Lorre farce without depravity and minors involved. Hilarious! Currently the best theme song, too.
Uh oh, I've run out.
So, honorable mentions---
The Mentalist (CBS) A House clone, except the House character is likable enough to believe people haven't fired or arrested him.
Sanctuary (Scifi) In the dictionary under "guilty pleasure." Dumb but imaginative and good hearted, unlike dull and mean, the preferred flavor.
Eleventh Hour (CBS) Interesting science, good lead actor.