More of a run than a graphic novel I guess but storytelling doesn't get any better than Alan Moore's time on Swamp Thing. If a story can make you wish you were a vegetable, how is it then NOT the best story ever written? Please, if you haven't felt feelings before or dream about forest fires, you need to read everything Moore's ever written about Swamp Thaaaang (a's added to sound cool).
As far stories intended to be isolated "graphic novels," then Ill have to go with Watchmen. I'm getting a little tired of it because it's everywhere now and Ive over talked it with people at this point, but new issues and connections are raised every time. It's a real masterpiece and showcase work for the field