I often look to Astro City for inspiration on this approach, because it's done such a great job with so many super-hero archetypes -- making them recognizable, yet retaining their own character in the course of the story rather than being another clone.
My topic for today example would not be another of the more iconic characters (Samaritan, Winged Victory, Jack-in-the-Box, etc.) but rather a misunderstood group of super-powereed beings: The Crossbreed.
Perhaps not that obvious when you first encounter them, but after thinking on it for a while you realize that they're the "misunderstood team of freaks or outcasts" exemplified in popular comic culture by the X-men and the Doom Patrol. Here's the official spiel from the Astro City website:
The Crossbreed — known derogatorily as "The Jesus Freaks," the Crossbreed believe their powers come from God, and are to be used in his service. Led by the enigmatic storm-casting Noah, the Crossbreed include the leonine Daniel, the rock-shaping Peter, the winged, angelic Mary, the giant David and the sonic-powered Joshua.
I'm particularly impressed by the selection of the "Jesus Freak" angle, because it allows a lot of X-menish riffs:
- the cross paralleled with the ubiquitous "X" naming of the X-teams;
- the symbol of the cross on their costumes again paralleled with the stylized "X" costumes;
- the religious dress used as the costume template, similar to the early x-costumes;
- the label "Jesus Freaks" as a way to rationalize their outcast nature (without necessarily pushing them to the 'hunted and feared' extreme of our favorite bunch of mutants)
Another thing that I liked was the way they tackled superpowers and codenames: none of them have the direct abilities of their namesakes, but rather from other abilities associated with their namesakes' stories. For example, Noah has storm-based abilities rather the ability to build boats or perhaps gather animals of different types together; likewise, David isn't necessarily skilled with the sling, but can grow to goliath size; and so on.
And much like their predecessors in the comics world, they show that they're much more that the caricatures they're made out to be by popular sentiment and the press.
Usage in superhero campaigns
Instead of the somewhat confusing fear of mutants in a world where aliens and other meta-humans are capable of just as much damage, the shift to a given religious, cultural, or political stance as a rationale for the 'hunted and feared' team is very useful. However, there must be ample reason to fear these ideological differences in a modern day and age -- or at least some reason for hostility from some quarters of the general populace. Perhaps they espouse controversial stances (for or against) the government or the major religions of your chosen setting?
If the team is a team of PCs, they're of course misunderstood -- they must strive against the stereotype to be recognized (or not) as true heroes. If they're NPCs, then keeping the PCs guessing the true intentions is key to retaining tension in the game.
Usage in Fantasy RPGs
It's not so much a stretch to borrow from this in Fantasy settings either. Perhaps the clerics of a given religion espouse controversial views on key issues (genocide, the treatment of men/women/children in society, other races, imperialism, etc.) but at the same time wield great power (clerical spells) and as such aren't seen so much as your friendly neighborhood priest or pastor, but rather a strange and aloof master of mysterious arts.
In a stunning reversal, the mad mages and alchemists of the genre could actually be the preferred and more approachable go-to groups for supra-human intervention and healing, rather than the clerics because of this distrust of the clergy.