1. "Year One" (Batman #404-407)
Whatever aspects of the Batman character weren't already re-defined by Frank Miller in his Dark Knight Returns series were done so with this landmark new origin for Batman, courtesy of writer Frank Miller and artist David Mazzucchelli.
The story tells the tale of Bruce Wayne and James Gordon, and how one man became Batman and the other became the symbol of honest cops in Gotham City (Harvey Dent also plays an important role, but Batman and Gordon's stories are the main ones in the story).
Originally, Bruce tried to be a vigilante without a costume. It did not go well. He barely gets home alive and that's when a new idea comes to him...
That this story was the basis for the blockbuster film, Batman Begins, is of no surprise, since Miller writes the story in a totally cinematic style, and Mazzucchelli's brilliant artwork certainly has a cinematic style to it, as well.
This is especially evident in the way that Miller uses the passage of time via calendars. Check it out in this legendary sequence from the second issue of the story, as Jim Gordon tries to get extra support to take down Batman but his superiors ignored him...
What a great use of the passage of time.
Perhaps the most impressive aspect of the comic is just how strong of a character Jim Gordon is in it. He truly works as the co-lead of the story. While writers certainly had done solo Gordon stories before this storyline, never had he gotten the attention Miller gave him, and a result, Gordon HAS had the same attention since.
Richmond Lewis' colors should get some attention - she does a marvelous job setting the mood. Very evocative washes.
Add it all together and you have an engaging and entertaining new origin for Batman as we see him go from green vigilante to a trusted friend of the Gotham City police (as the police also go from being totally corrupt to only being significantly corrupt - a major step up!).
NOTE: The votes between #1 and #2 were the closest I've ever seen on one of these polls. They were separated by less than five points total. Just crazy.
That's the list! I hope you all had fun with it!