[trebleshot]

Wow, that's a tough question for me. I guess I could narrow it down to some of my favorites:

Uncanny X-Men: debut of Hellfire Club; Giant-Sized X-Men #1
Ultimate Spider-Man (at least until #80, when I stopped reading/collecting comics on a regular basis)
Transformers #1-80
Joe Kelly's run on Deadpool
Original Age of Apocalypse series
Onslaught saga

There are probably others I can't think of at the moment, but that's still a good list.

EDIT: Add the Earth X/Universe X/Paradise X trilogy. It's basically Kingdom Come for the Marvel Universe. Also, there's the Marvel/DC crossover that led to the creation of the Amalgam universe. Loved that too.