I have a difficult time deciding which show is the best of all time (too many good shows for that!)
That said, I was very, very impressed with Breaking Bad. For all the things it does right, I keep coming back to character development. The main protagonist becomes the antagonist and the lines of morality get so blurred it's hard to tell right from wrong anymore. The finale left me hollowed out and stunned for a few days. For the record, I think Walt is a wicked human being.
I also love the revamped Doctor Who, although it has started to lose its charm for me (series seven went way downhill, yikes.) Hope it picks up again.