I need to be pair my list down a bit and even ignore some stuff, I am thinking more about collected editions and trades as runs.
Here is a paired down list:
1. Jim Shooter and George Perez's Avengers, especially the Ultron and Count Nefaria runs.
2. Jim Shooter and Curt Swan's Legion of Superhero Stories, from the Fatal Five all the Way to the Ghost of Ferro Lad.
3. Batman by Rodgers and Englehart,
4. Cary Bates and Elliot S. Maggin, "Who Took the Super Out of Superman" though I kind of love Superman from about 290-320, but maybe 400?
5. Kurt Busiek, Alex Ross, Brent Anderson: "Astro City", its probably the Jack in The Box saga or Tarnished Angel.
This is really tough, I love the first 10 issues of the FF and the first 10 of Ditko Lee Spiderman, just great villain after villain stories.