Are they brown due to stain in the bone, or are they coated with a really thin brownish membrane? In either case, soak them in some water for a couple of weeks, or longer if necessary. If it is blood stains, the water will draw them out of the bone. If it is the membrane, the water will loosen it up and you can then peel it off the skull. Once the skull is finished cleaning, just rinse it off with clean water and let it dry in the sun. Do not peroxide it. This should leave the natural bone color to the skull.
