There are of course the MnM published adventures, but barring that you can go with ideas from the comics:
For a Campaign:
The PCs are all B-grade supervillans. A group of uberpowerful A-listers is martialing an army of villans and they approach the PCs, all of whom have reasons to not want to join. Now the PCs must band together to save themselves.
The PCs all come from different realities, they have been recruited by an extradiminsional entity to "fix" broken worlds. This might work particularly well if all of your players were ubercomic geeks who know all the details of one companie's universe, giving you pleanty of room to play with.
A supervillan's grand plan has almost utterly destroyed the City, most of the people have evacuated and the federal government is blockading it to keep the villan's creations from getting out. However, about 20% of the population has decided to stay for various reasons, or were unable to get out. The PCs have elected to remain, defend their city, and ultimately restore it to its former glory.
The Supervillan Prison experiances the worst break out in history. Now there are 52 of the evilist, vilest, baddest bad guys in the world roaming free. The PCs are tasked to brign them back in. Have them all start as superpowered guards at the prison, all of whom leave their post to fight off an attack that turns out to be a diversion so that the escape can take place. That way they have a more personal motive to bring the villans back.
More Generic Adventures:
-Evil dopplegangers of themselves come from the negadiminsion to wreak havoc on a new world. Or reverse it and strand them in the negadimension.
- Innocent civilians are turning into hi-tech hero hunters. The PCs have to stop the civilians w/o hurting them and find out who is behind it.
- A former world renowned champion turns out to be the scout for an alien invasion. He has gotten the drop on the World's Greatest Heroes and its up to the PCs to stop him.
- An advanced alien race gathers champions from a dozen worlds and forces them into gladitorial combat. The PCs must not only win every match, or risk an alien strike against earth, but figure out a way to free themselves and the other captives.
-The supervillan Dr. Umbra, long thought dead, is back. Unfortunately Solaris, his heroic nemesis, seems to have stayed dead. Who will stop him from covering the city in an impentrable dome of night?
-A demonic cult is working from ancient plans of the city, planting explosions to destroy buildings to form a summoning glyph for their demonic master.
Just to name a few.