Skulls as Hirogen trophies
The skull of a Xindi-Avian
The skull was the framework of the head in most animals including humanoids. The skull protected the brain and had sockets for housing the eyes. It was part of the skeletal system.
Gallamites had transparent skulls. (DS9: "The Maquis, Part I", "Let He Who Is Without Sin...", "Resurrection", "Penumbra")
Data and Worf found at least two skeletal systems including the skulls in disfunctional cryogenic chambers aboard the cryonics satellite in late 2364. (TNG: "The Neutral Zone")
Doctor Noonian Soong kept a Human skull and the skull of a Tyrannosaurus rex in his laboratory on Terlina III. (TNG: "Brothers")
Data's skull was composed of cortenide and duranium. (TNG: "The Chase")
Cranial implants were installed into the skull. When Doctor Julian Bashir said to Odo he thought he knew of these cranial implants, Odo joked he was never able to view into a Cardassian skull. (DS9: "The Wire")
Both Hirogen and Kazon keep the skulls of slain victims on trophy walls aboard their starships. (VOY: "Initiations", "Hunters", "Prey")
Doctor McCoy also kept several alien skulls in his sickbay. (TOS: "The Conscience of the King")
Quark once had damaged bones in the back of his skull repaired. (DS9: "Take Me Out to the Holosuite")
Terran Empire MACOs used the skull as a symbol. (ENT: "In a Mirror, Darkly")