I have found that trying to include together on one list the truly best television series I've ever seen invariably leads to a list heavily laden with recent series. I once thought that this was recency bias. However, in the fullness of time, I've come to realize that it is generally because television has become progressively better and better. Comparing (for example) series from the 1990s against those of the 1970s still yields a list heavy with 1990s entrants. There are some older series that are sentimental favorites, but when I really dig down into the fundamentals (quality of acting, writing, directing, photography, art direction, set design, etc.) more recent series beat-the-pants-off older series, every time.
The Wire is very high on my list, but it is not at the top because, as good as the acting was, the writing suffered as the series went on, as the production team struggled to make each season interesting in its own right, and unfortunately doing a lesser job in a couple of the seasons. By comparison, Sleeper Cell was everything that The Wire should have been, suffering only from coming after (and therefore not getting points for being first, with many aspects of the production) and a much shorter run (only two seasons). It sits firmly at the top of my list.
Hill Street Blues is in some ways one of those sentimental favorites, and perhaps the oldest series that ranks very highly. The sentimental boost it earns comes from the fact that everything before Hill Street Blues was inferior because of a reluctance for Hollywood to be generally realistic in its portrayals. Hill Street Blues made it safe to have flawed protagonists.
The Shield is definitely on the list. It took the flawed hero one step further, and was the first of a number of riveting series that cable has provided that are, collectively, better than what broadcast television has ever provided us: Deadwood, Breaking Bad, The Americans, Sons of Anarchy, Dexter, Prison Break, etc. The problem here is that if I considered all of the shows that followed on from The Shield, they would fill the list, pushing out all of the older series shown below. Again: Television is far better today than it was in decades past.
The West Wing had the best overall run, including a fantastic way of closing the story at the end. It projected what I can only believe is the same kind of optimism for the future that living through the Kennedy administration projected, and was the perfect combination of smart, funny, and interesting.
Lost was the series with perhaps the best overall arc, though it often found its mythology muddied by unnecessary complexity and missteps by the production team. However, its overall accomplishment more than made up for that.
Between Firefly, Babylon 5 and Battlestar Galactica, I feel that there is at least one, if not two great series there, but it is hard to really put myself behind any one of the three series above the others. Firefly perhaps could have been great, but it really was cut too short to have distinguished itself in my mind. Battlestar Galactica was quite remarkable, presenting a thoroughly satisfying many-year arc. However, I think Babylon 5 has to be recognized as the best long-running space story ever told on television. It was structurally almost perfect (damaged only by the scare at the end of its second-to-last season that that would be the end of the series). It's biggest problem, actually, was that the series was the recorded on video rather than film, and just before the digital revolution, and so what we have today is one of the best space series that simply doesn't show well in HD.
24 is back, a testament to how good it is. It does come across as a bit formulaic, but that can be balanced by a recognition that when the formula works, every single time, as it does with 24, then don't mess with success. Jack Bauer has become a part of society's lexicon.
Alias had the best first season and a half of any television series with a long-running arc. I feel the show lost a lot after that, but through the point in time when SD-6 was taken down, the show was practically perfect.
Buffy The Vampire Slayer is very high up there, not because the show was perfect, but because it paved the way for high quality drama deliberately aimed at a youthful audience. It turned a whole genre from vacuous puff into something worthy of being watched. Fans of the show are torn about whether the show should have ended after Season Five or not - that results in a much more perfect series, as such, but would have excluded the two best episodes of the series (Hush, and Once More With Feeling).
Six Feet Under deserves a mention if for no reason other than its presenting the single best final five minutes of a long-running series. Putting aside all the other great things about the series, it was all made worth it with the piece of art that was its closing sequence .
The X-Files is a hard one: Most of it was quite good, but I do feel that in trying to go back and forth between being a mythology show and not being one something was lost.
Heroes also might be up on the list, but quite frankly after the first season it sucked.
I do put Friends up on the list, though I feel that it, like Seinfeld, doesn't stand the test of time. As it was being broadcast though, it provided a great mix of comedy and characters that you really came to care about.