I've only recently started in on graphic novels. The Sandman series is good, but a little uneven, I find. For mine, Watchmen is a little overrated, but that might have been the weight of expectation. The Dark Knight Returns had nothing on The Long Halloween, which I thought was fantastic - I'm hoping the Harvey Dent storyline is worked into Nolan's The Dark Knight. And I really liked Marvel 1602, until... well, that would ruin it. But for the most part it was good. I've a lot of readign to do before I can venture a 'greatest' nominee, though.
Oh, and just started in on Fables, which I'm really liking.