Here are the superhero campaigns I've run:
(1) A standard Marvel campaign back when the MSH RPG was new. I stuck to continuity as much as possible (though a few months behind, just in case). The PCs got to interact with various current events like the X-Men's fight against Nimrod or the Mutant Massacre. There were lots of neat things happening in this world, including a couple of players in the main campaign making extra characters for solo campaigns taking place in the same world. Eventually, the game ended when one of the solo campaigns involved a player playing a villain who tried to outsmart everybody, but Dr. Doom ended up outsmarting him too, and Doom took over the world.
(2) A "New Universe" style campaign back when the "New Universe" was new. I modeled the game after the DP7 comic, with characters knowing only their pre-powered stats and having to figure out how their powers worked and what they could do. But I actually made many changes to the "New Universe" setting to make it more palatable to me, and eventually it lead to a spin-off campaign...
(3) The spin-off campaign featured the players playing themselves with powers traveling through various alternate universes. The game switched from the Marvel RPG to the various games put out by Chaosium (including Superworld for superheroes, Call of Cthulhu for the Cthulhu-inhabited universe, Elric/Stormbringer for that universe, etc). Things got very complicated very quickly (especially when one player gathered an army of superheroes to fight another player who had gone insane and fallen under the control of a villain who gathered/created his own army of villains, including a dhole with a Green Lantern power ring), and I discovered that I really needed a game that could handle superheroes better than Superworld, so I switched to the DCH RPG which worked far better. That campaign lasted until one of the PCs asked a knowledgeable NPC about the nature of reality which required that the PCs not know its nature or it would cease to exist. The PCs barely survived that experience but their multiverse was gone, sending to another multiversal experience, using a different game system for each universe. However, by this point, I was down to two players and one wasn't that interested in the new multiverse, so that lead to a new campaign.
(4) A totally homebrew campaign, where the idea was that every hero only had one power (though it might be multiple powers in the game system), and that power was somewhat unique (somewhat like Xanth). That campaign didn't interest the players as much as past campaigns probably because it forced them into the standard "wait for something to happen and deal with it" roles that I certainly find boring. They at least played through one last adventure involving time travel that explained the origin of superpowers on this world.
(5) My next campaign involved the players again playing themselves on a world where nobody had powers. But then, a threat to the multiverse arrived and started to destroy their world. This threat happened to take souvenir "patches" of each destroyed world and put them together in a patchwork world where the PCs ended up adventuring. However, they had another problem to face. When the threat arrived on Earth, his minions powered up each PC and made them evil. A dying wizard arrived in time to split the PCs into two people: one evil and powerful, the other being their normal selves with their normal personalities. So, they had evil twins to deal with who had phenomenal powers. Thanks to the wizard, the PCs got a head start of about a week in which to try to gain powers and magic items and so forth. However, the central draw for the players was the fact that the powers they were *slowly* gaining (and the powers that their evil selves had) were the same powers, abilities, and weapons that belonged to their favorite characters. Eventually, the PCs won, defeating their evil twins, but they ended up having attained strange and unusal bodies and powers at the end of their battle, and not all of decided to return to Earth. (Only 2 out of 5 did. The other three found places on the patchwork world to live on.)
And then after that, everyone moved away (including me), so I haven't had anyone to play superhero games with. My current gaming group isn't too open to new experiences, preferring D&D and not much else (at least one player won't play anything but D&D and he's one of the few people who can be relied on to always show up).