When I was first coming up with this list, the hardest part was coming up with an order. That is probably not surprising since many of the stories I listed are so different that they are hard to compare. I had no problem picking number one though. Maus is my absolute favorite comic story.
Maus is very different from most of the comics on the list. For one thing, it is non-fiction. Maus is the story of Vladek Spiegelman, a Polish Jew who survived the Holocaust. It also recounts the difficult relationship Art Spiegelman had with his father, mostly in describing the interviews Art had with his father about his experiences during the war. This is later complicated by the fact that his father dies between the first and second volumes. The writing is emotional, raw, and real. Unlike the neat little packages of fiction, Art never seems to come to terms with how he feels about his father.
In a stroke of genius, Art Spiegelman chose to present all of the characters in this biography as anthropomorphic animals. The Jews were all mice, the Germans cats, the Poles pigs, etc. He used this artistic conceit to great effect on many occasions, like when Vladek and his wife Anja are trying to masquerade as Poles to avoid imprisonment. During these sequences, they are shown as wearing cheap Halloween style pig masks. This simple artistic trick highlights how precarious their situation was and how easily a single misstep could bring ruin.
Maus is an example of the heights to which comic books can rise. Like prose or video, comics can be used to tell any type of story. There is no reason for the medium to be limited to stories of over-endowed spandex wearing super-humans beating on one another. As Scott McCloud points out, the focus of American comic books on superheroes is more of a historical fluke than anything else.
Maus is a truly shining example of the best comics have to offer. I just hope that some day, the rest of the medium will catch up.