I was more partial to Marvel Comics growing up, so my answers are going to reflect that. I don't mean to imply that DC, Dark Horse, or the others didn't make good books.
Anyway, here are my fav's in order:
Secret Wars: Very, very fun. The first time all the main heroes got together to battle all the main bad villains. The story was simple: Marvel's greatest heroes and villains are transported to a synthetic world by the Beyonder, who wishes to observe good and evil in action. What we have is the battle of the decade. Of course it was really campy, nothing that interesting. One thing of note- that's where Spider Man got a certain black alien costume.
Inferno: There was sooooooo much backstory, it would take forever to explain it all. Let me sum up. The demons of Limbo are out to overtake the Earth by opening a portal between dimensions. While New York struggles to deal with hell on Earth, the heroes fight to drive back the demonic horde. The X-characters (X-Men, X-Factor, New Mutants) were the main people battling back the baddies. New York-based heroes got their crossovers, but Spider Man and the Avengers just beat down some demons and that's it. No big effect on the story. Over all, to that point, it was the first really violent and dark storyline I ever read. I really liked it.
Infinity Gauntlet:Thanos acquires the Infinity Gauntlet, a glove with six gems of unimaginable power sewn into it. After using the gauntlet's power to reshape reality to his liking, he finds himself in battle with both the cosmic beings and the superheroes, who prefer things the way they were. I liked it. I think the other one-shots it spawned were weak, Gauntlet was pretty cool.
Evolution War: Convinced that the human race needs his help to reach the next stage of its evolution, the High Evolutionary launches a series of plans to prepare humanity for his benevolence.
Atlantis Attacks: Ghaur returns to Earth to complete his ultimate goal: the resurrection of the evil god Set, who is depicted as a giant serpent with seven heads. To that end, he enlists the help of the unwitting Atlanteans, who attack the surface world while he makes the preparations needed to welcome Set back into this dimension. Eh, it was ok. Nothing memorable.
All of those were awsome story lines... However I think you forgot one.
SpiderMan Clone Wars. Spiderman faught with a clone a while back and won, however it was actually the clone who won, and all this time it was him who assumed the iddentity of Spiderman, fighting crime and marrying Mary Jane. Then the original comes back. (I don't remember completly if this was the story line but i think iw was something like this)
There are 10 types of people in this world. Those who know binary... and those who don't.
How could you forget the Onslaught series ? it's the one when Professor X goes crazy and with the help of Magneto and Franklin Richards becomes a mega powerful entity and tries (and almost succeeds) to destroy the world.
Onslaught came out after I stopped collecting, but you're right, that is a big one. I remember hearing that they were sending a lot of the non-mutant heroes into a seperate universe. Crazy. I'm glad they brought them all back.
One of my all time favorites were Crises on Infinite Earths by D.C. that paticular crossover cleared cup a lot of discrepincy over all of the mulitipule D.C. universes.