The Eisner awards is the Academy Awards for comic books. It has given recognition to the greatest comics and writers.
For me the top 3 stories I can't believe didn't win are:
Superman: Red Son - Nominated for best limited series but lost to "Fantastic Four: Unstable Molecules"
Geoff Johns for his GL work
Note - The Eisner Awards came out in 1988.
Note- While the Eisner Awards isn't the only Comic book awards, the easiest way to think of it is comparing The Academy awards to the MTV movie awards.