The Wire is perhaps the easiest program to put at the top of an "all-time best" list. I think, though, that I'd put
Sleeper Cell above it, mostly because it was tighter (only two seasons, while The Wire dragged a bit in the middle of its five seasons).
Six Feet Under and
The Sopranos are both also excellent programs. The two shows split complementary distinctions: Six Feet Under having one of the best endings of any series, while The Sopranos having arguably the most unsatisfying.
Deadwood was also a superior program, as was
The Shield.
Dexter is perhaps one of the best shows still being broadcast.
There are two obvious trends we can see from how this list is developing. First, death is a featured theme for all of these shows, and each of these shows were exceedingly depressing at times. The ability for these shows to evoke such emotion was part of their excellence. However, I think we really need to include some happy shows on a "best ever" list, to stave off unrelenting maudlin. 
The other obvious trend is that all but one of these shows were presented on premium cable networks: People had to pay about $10 per month to see these series uncut and in first run. I believe a firm argument can be made that premium cable has provided a path to provide the quality of the very best feature films on the television medium, but also does so in a manner that fosters the long form (13 hours a year) in a way that the feature film genre never could. While we don't subscribe to premium cable any more (we pick such shows up on disc a year later, now), I have to acknowledge that premium cable is the greatest force for superior entertainment, today.
I cannot put together an "all-time best" list without including
Hill Street Blues, the show I personally feel signaled the quantum leap in quality of television dramas. 1981 is when television really started getting great, and Hill Street Blues was at the vanguard of that renaissance.
What Hill Street Blues signaled for drama, I believe
Soap signaled for comedy. While I don't think comedy has made quite the same leap as drama did, Soap opened a lot of doors to excellence, which occasionally we see some programs capitalize on. And I cannot mention comedy without mentioning
The Simpsons. Due to its longevity, it is a favorite target for underrating. After well over two decades, though, it remains sharp and superior.
While
Lost is arguably our favorite "non-death-themed" program, I am still undecided about whether it belongs on a "all-time best" list. There is a difference, I feel, between a show we feel driven to watch religiously, because we want to see where it goes and how it gets there, and a show that will truly stand the test of time. I'm also not sure about
Battlestar Galactica. While it was superior television while it lasted, I wonder about how I'll feel about it a few years down the road.
Indeed, genre programming with strong story-arcs (a category that applies to both Lost and Battlestar Galactica) seems to sometimes focus more on getting to the destination than the journey. An "all-time best" really needs to be about both. Both Lost and Battlestar Galactica are great, but I think could end up eventually falling off of "best".
Babylon 5 probably does belong on the "all-time best" list, but I worry about its poor CGI production values. For now, the biggest stand-out in genre programming is
Star Trek: The Next Generation and
Quantum Leap: Neither reached as high as Babylon 5 did, from an effects standpoint, but as a result both will surely weather time better, given their excellent stories and characters.
Shows that just missed my 15 "all-time best" list include The West Wing (which made us believe, if only for a short time, that government could actually inspire), 24 (impressive in many ways, but most of all because it is essentially a one-man tour de force), My So-Called Life (the shortest-lived best show ever), and Wiseguy (perhaps the most underrated show on this list).
I like BURN NOTICE but this past "season" was a bit boring, hope next "season" livens up a little. I also watched DAMAGES the first season, but kind of got lost in the second, but it was a great show. Acting on that was superb. TRUE BLOOD is another one I like, as is NURSE JACKIE. 
