Skulls can be obtained from the corpses of dead creatures and as a by-product of butchering. Most creatures have one skull, including - amusingly enough - seven-headed Hydras!
Skulls can be processed into totems at the craftsdwarf's workshop.
Unlike bones or shells, dwarves never request skulls for strange moods.
For totems, the value of the original animal is very important. Like all creature byproducts, the skull value is scaled by the modvalue of the creature.
Occasionally, the violence of combat can remove a head from a corpse. This can be left to rot underground to produce a skull, or be butchered for 1 meat and a stack of 1 bone.
Note that leaving any such parts to rot on a tile defined as "Above Ground" will cause any skulls or bones to vanish over time.