I forgot two of my favorite tales of the multiverse:
Squadron Supreme, No. 1-12
After freeing their world from the rule of the evil Overmind, the Squadron Supreme, the greatest heroes of an alternate earth in the Marvel Universe, set about the task of repairing the damage that they helped inflict while under the Overmind’s control and restore the world to the way it had been. However, the question arises, “Why stop there?” Resolving to build a better world, the Squadron launches Project Utopia, and begins the year-long process of turning Earth into a Paradise free of the ills that had once plagued it. Unfortunately, they soon find that freedom is the price that has to be paid in order to make the world perfect.
What If...? Vol. 1, No. 32, “What If The Avengers Had Become Pawns Of Korvac?”
In “The Korvac Saga,” the Avengers faced off against Korvac, a being of godlike power who intended to impose his own vision of perfection onto the universe. While on Earth 616, the main Earth of the Marvel Universe, Earth’s Mightiest Heroes managed to achieve a costly victory and defeat Korvac, but what if Korvac had been triumphant and been free to pursue his dream of a universe united under what he intended to be his benevolent rule and had recruited the Avengers to help him achieve it?
With Squadron Supreme, you kind of get two multiverse stories in one. While the Squadron was a group of heroes on another Earth in Marvel’s multiverse, they were also created as something of an homage to DC’s Justice League of America. Writer Mark Gruenwald always wanted to write a Justice League story, but, sadly, he never had the opportunity in his too-short life. However, while some of the names and backgrounds might have been different, it seems to me that with this book he managed to write a pretty damn good Justice League story anyway.
One of my favorite aspects of the Korvac story is that you actually get to see the fabled Ultimate Nullifier put to use.
I should also mention that the multiverse played a very important role in the stories in Captain Britain, as presented by Alan Moore, Jamie Delano, Alan Davis, and Chris Claremont, which I enjoyed a great deal. So call that an honorable mention, I guess.