One of the biggest challenges for any crossover story is compiling more than one character that may have one or more thing in common such as being within the same realm of existence. These are some examples of multiverse crossovers that could work if dealt with great care:
WWH/World War Hell (Hellboy, Constantine, Devil May Cry, Spawn, Ghost Rider): All characters have dealt with the occult and the forces of hell. So what better way to have these heroes working together than having to settle a civil war in Hell?
Galactic Crisis (Halo, Mass Effect, StarCraft, Star Trek -Generations preferably-, Star Wars -Clone Wars or Galactic Empire-): Given how each of these franchises have a bigger threat to deal with (Star Trek with the Borgs, Halo with the Flood, Star Wars with Abeloth and the Yuuzan-Vong, Mass Effect with the Reapers and StarCraft with the Zerg swarm) it would be a sci-fi geeks dream come true to see all these characters fighting these massive threats or just one controlling the others (maybe like the molding of the Gravemind, Abeloth and Kerrigan the Primal Zerg together as a great threat to everyone else. Whether dealing with each of their adversaries together or individually, the heroes from each series can work together to bring peace to the final unexplored frontier known as space. Sort of inspired by the crossover film Galactic Battles.
Ultimate Fight Tournament (Street Fighter, Mortal Kombat, King of Fighters, Killer Instinct, Final Fight, Tekken): This would be the most epic fight tournament we'd ever see in a crossover. The plot could be that Shao Khan, through Quan Chi and Shang Tsun, brings the other realms of the other franchises before mentioned for the tournament to end all tournaments in another attempt to conquer new worlds and obtain more souls. Raiden and his allies attempt to prevent this by warning the various characters of said universes as they race to stop their foes from victory. This crossover could work in having the other characters getting their own fatalities and we would get to see matchups we'd never fought we get to see like maybe a three way fight between Chun-Li, Mai Shiranui and Katana or an all-out brawl between Heavy D!, Balrog, TJ Combo and Dudley.