The best way to watch a good t.v. series is on DVD.
Several years ago we started watching NYPD Blue every night on re-runs. We obviously had to tape some, but it was mostly one episode every night at 10:00 and we watched essentially the entire run (up to the point -- I don't think it had ended yet). It was a great way to watch the show because you were more invested in the story and characters and it was much easier to keep track of what was going on.
A couple of years ago we watched the first two seasons of Alias on DVD. The show was terrific, which of course helped, but I really enjoyed the process. One down side was that each episode ended with a mini cliff-hanger and it was very difficult, with the next episode right there with a click of the remote, to stop watching.
Since then we've watched a couple of other shows on DVD, like Veronica Mars and Friday Night Lights. We also re-watched classics like Undeclared and Freaks and Geeks, each of which only had a one-season run.
This weekend we just finished the 13 episode season one run of Damages, which Rachel got for her birthday on DVD. It may have been the perfect blend of content and medium. First, it was only a 13-episode season, so the time commitment was not as big as say the first season of Lost (which would have been great on DVD). But the show was really more like a movie (or mini series) than a t.v. show. Its plot was almost exclusively about one story line and there really weren't any characters to root for or to even like. Because the plot was so good, though it didn't matter. But over 22 episodes it might become tiresome to watch all of these bad people. It has just started a second season run (which we've DVR'd and intend to watch) so we'll see if the format holds up.