Yesterday after bring-in I went to work on it - I scrubbed her legs with EQyss Micro-Tek medicated shampoo and toweled them dry, then put some Nolvasan antiseptic ointment on the crusty places - I never try to pick these off but let them resolve on their own. I've also had good luck using Listerine mouthwash to treat mild cases of this sort of thing, as well as the crud horses sometimes get on the fronts of their cannon bones, or mild irritation/infections from bug/tick bites. I've heard that some people have had good luck with Desenex or even Balmex as a treatment/preventative. Of course the treatment needed may depend on what's causing the problem.
If you've had experience with scratches or rain rot, what treatments have you found to be effective?