I like the Batman sock idea.
This got me thinking, though...why would he wear boots in the first place? He doesn't wear gloves and he does a lot more with his hands than with his feet. He gets around by flying for Pete's sake.
Boots are just going to wear out and need cleaning. His feet are as indestructable as the rest of him and easier to clean. I have to conclude the boots must serve as part of the disguise. Does he have really gnarly bunions or something?