Here's a weird idea for how the worst disguise in superhero history actually works.
You've heard the jokes about Superman's disguise before. The difference between Clark Kent is, effectively, a pair of glasses, a slouch and a suit. Sometimes Clark wears a hat. But, really, if you can't see through that, there must be something wrong with you.
That's precisely where this new theory comes into play. What if, against all odds, Kal-El just spent most of his time around people with prosopagnosia -- face blindness? Prosopagnosia is a neurological disorder that places an extreme limitation on a person's ability to recognize and remember faces. People with this rare disorder (it only afflicts about 2.5 percent of people) rely on recognizing others by the way the dress, walk and other mannerisms. We know that Superman goes to great pains to alter these aspects of himself when he switches back and forth between being Clark Kent.
And if you're not convinced that everyone Clark works with just so happens to have a rare disease, consider that he might give them the disease. The condition often stems from lesions or other damage to the fusiform gyrus within the brain. Damage there makes facial recognition very challenging. So perhaps Superman is sneaking in on his sleeping comrades and performing a little heat-vision surgery. Boy, suddenly Superman seems like a horrible monster!
Of course, it could just be the Superman is a comic-book character. But why rely on simple explanations when we've got science?