Batman: New Gotham
Gotham emerges from No Man's Land, complete with new creative teams.
Spider-Man: Hobgoblin and the Black Costume
The original Hobgoblin and Alien Costume sagas, all bound up.
Superman (1999-2006)
Superman from Jeph Loeb and Y2K until Infinite Crisis and One Year Later.
Spider-Man: Big Time
Slott's run from 648-700.
Spider-Man: Brand New Day
When Spider-Man came out three times a month!
WildC.A.T.s by Jim Lee
Jim Lee's inaugural run of WildC.A.T.s in one volume.
Daredevil by Ed Brubaker
Two volumes to cover Brubaker's run. The Marvel Omnibus Editions almost got it right.
JLA: The Grant Morrison Collection
Two volumes of Grant Morrison's JLA plus a Companion!
Spider-Man 2099
Includes all Peter David issues in two volumes.
Countdown to Final Crisis
Two volume Countdown set.