Skulls can't be used for anything in the game, but they can be sold to some stores for 1 GP and you need one skull in the subquest that will transform Melicamp back into his normal form. Skulls are dropped by skeletons.
In Beregost, skulls may be sold in Feldepost's Inn.
In-game description
| “ | This appears to be the skull of a human. | ” |