Even though this isn't anime or manga, this seems most appropriate here.
Amazon.com: 40 Years of the X-Men: Software
Amazon.com: Amazing Spider-Man Complete Comic Book Collection Win/Mac: Windows XP Home Edition: Software
Amazon.com: Fantastic Four and Silver Surfer - Complete Comic Edition: Windows & Macintosh: Software
Amazon.com: The Invincible Iron Man: The Complete Collection: Software
Course, you still miss a good bit. For example, New Mutants, X-Factor, X-Force, the Ago of Apocalypse books, and most crossovers. However, man, is this a good deal. It should be easy(in comparison) to fill in the gaps.