If it's just that they're discolored but otherwise dry and free from meat/gristle, I soak skulls in a bath of oxyclean and hydrogen pyroxide. That has gentle bleaching agents in there that both loosens dirt and whitens the bones.
I left a couple of deer skulls soak in a five-gallon bucket of bleach for a week. It loosened the dry bits of meat still attached and made them brighter. Of course I'll probably stain them when I actually get around to using them.
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