Title: Marvel vs DC
Year: 1996
Apparently two god-like brothers embodied the Marvel and DC universes. They had been unaware of each other until various cosmic events and Crisis's awakened each to the others presence. They began fighting, threatening the existence of both universes. In the process characters from both universes fought each other.
To save both realities they joined into one universe known as Amalgam, where characters from both companies were merged into new characters. Wolverine for example, was Dark Claw, protector of Gotham, Bruce Wayne was a Shield agent, Superman and Captain America were now Supersoldier, and so forth. Marvel and DC co-created (and thus Co-own) the character Axel Asher, known as Access. Access simultaneously exists in both Universes. In the Amaglam universe, only Access and Dr. Strangefate (A combination of Professor X, Dr, Strange, and Dr. Fate) know this world is an Amalgam of two others. Dr. Strangefate wants to maintain this universe, while Access wants to re-separate them.
Access won, and the two brothers realize their conflict is pointless. Access continues to live in both universes and if he stays in one too long, the two will start to overlap, causing a crossover. Access's job is to make sure the Universes stay separate.
In the miniseries All Access, Dr. Strangefate re-emerges, as he was hiding in Dr. Strange's subconscious. He recreates the Amalgam universe, but Dr. Strange managed to place the entire universe in a pocket dimension so that it could exist without threatening the Marvel and DC universes. The pocket dimension is stored in a vessel that Access has for safe keeping.
Access also appeared in Green Lantern #87.
For More on Amalgam, click here.
Title: Deathmate
Year: 1993
Solar from Valiant comics finds and falls in love with Void from Image comics. Their love makes a world combining the two worlds, but is unstable. The heroes of this world must re-separate the two universes to save all of reality.
Title: JLA/Wildcats: Crime Machine.
Year: 1997
The two teams fight the Master of Time. Also known as the Dark Nova event.
Title: Devils Reign Marvels Mephisto realized no body ruled hell in the Top Cow universe, so he sought to take over. Marvel heroes teamed up with Top Cow heroes to stop them.
Title: Shattered Image
Year: 1996
In this story, worlds from the six studios that formed Image comics each separate into their own reality. (As opposed to merging worlds as other crossovers do.)Actually the story shows that the Extreme Studios reality had already separated. (As founder Rob Liefield already left the company by this point.)
Title: Smoosh Image
A parody/tribute to the Marvel/DC Amalgam, where various Image characters are merged together.
More about Smoosh can be read here.
Title: World War Three
Year: 1997
The Wildstorm Universe fades temporarily out of existence as Marvel's Heroes Reborn world is about to end. The two merge in a world where Dr. Doom, the Daemonites, and the Skrulls ally against earth. The reality is ended when Reed Richards of the Fantastic Four manages to separate it in the Negative Zone.
More about World War 3 can be read here.