My all time favorite would be probably Battlestar Galactica, the other contenders being The Wire and Deep Space Nine.
I considered The Walking Dead (I guess it's current), but after six episodes (not all as good as the first couple) I'm not sold. Breaking Bad intrigues me but I haven't seen it yet, nor have I seen Game of Thrones. Community is close but I'm not a comedy guy. House used to be up there but it isn't what it used to be. There's a fair number of excellent but not transcendently great shows (e.g. Castle, Burn Notice, Fringe), but I wonder if the truly top quality television hasn't taken a dip recently (or if I'm just missing something). I'd take the Daily Show over the Colbert Report, but I watch both.
My currently running favorite (to actually answer the OP) is probably Treme.
It tackles a tough subject with grace and has a similar sense of authenticity to The Wire. The way music is incorporated into the show is really unique and entertaining.