1. Kingdom Come
One of the greatest Superman stories by Mark Waid and Alex Ross. I love how the Book of Revelation acts as a theme to Kingdom Come.
2. The Return of Superman
Four Supermen? Superman returning from the dead? The introduction of Superboy and Steel? What more could anybody ask?
3. Whatever Happened To The Man of Tomorrow
Alan Moore did an outstanding job ending the silver age era.
4. Superman: Peace On Earth
Great story by Paul Dini and Alex Ross where Superman tackles something that is more difficult than fighting a villain---- world hunger.
5. Superman: Last Son
From directing Superman: The Move to writing Last Son, Richard Donner along with Geoff Johns has done an outstanding job tackling where it was possible for Superman and Lois to have a child and reintroduce General Zod into the comics.