Animal skulls are never used for phrenology and you can safely turn them into fertilizer or whatever.
Aberration skulls will eventually be used in aberration phrenology. Basically any sentient monster type's skulls will be useful for phrenology, so crone-kin would work that way as well.
Demon, aberration, and crone-kin phrenology are probably only going to have recipes at high level, though (70+), so it will be a while before they're actually useful. I would sell them, personally, because there will be a whole lot more of those monster types at high level and so the skulls will be easier to get.