Here is a list of my favorite story lines from the Marvel Comics universe. They are listed in chronological order by year of when the story happened.
1. Secret Wars
Writer(s): Jim Shooter
Summary: The Beyonder transports Earth’s heroes and villains to Battleworld to fight for his amusement.
Writer(s): Chris Claremont & Louise Simonson
Summary: Revolves around a demonic invasion of Earth and centers on the fight between them and the various mutant factions.
3. Suicide Run
Writer(s): Chuck Dixon, Larry Hama & Steven Grant
Summary: Punisher is thought dead after he explodes a building full of mobsters on himself. Punisher copies come out of the woodwork.
4. Age of Apocalypse
Writer(s): Scott Lobdell, Mark Waid, Fabian Nicieza, John Francis Moore, Larry Hama, Warren Ellis, Jeph Loeb, Howard Mackie & Terry Kavanagh
Summary: Deals with the ramifications of Legion traveling back in time to kill Magneto only to end up accidentally killing Professor X instead.
Writer(s): Jeph Loeb, Mark Waid, Peter David & Terry Kavanagh
Summary: Onslaught, a psionic being combining the psyches of Professor X and Magneto lays waste to the entire Marvel Universe.
6. Welcome Back Frank
Writer(s): Garth Ennis
Summary: The Punisher returns to dispense his own brand of justice on the streets of New York City.
Writer(s): Chuck Dixon
Summary: Victor von Doom is trapped on an alternate Earth and fights to get back to his home world.
8. Dark Reign
Writer(s): Brian Michael Bendis
Summary: In the aftermath of Secret Invasion, there is a shift of power toward Norman Osborn, who takes over SHIELD and begins to carry out his own twisted agenda.