Piles of bones composed of... well... Nothing but Skulls. The rest of the bones vanish without explanation. It doesn't matter whether the victims were killed by ancient death traps, man-eating monsters or barbarian hordes; nothing remains but the skull.
There are good narrative and practical reasons for this. A human skull is instantly recognizable, making it a powerful symbol of death. Other bones do not carry the same emotive weight; few people could identify a human shoulder blade on sight.
It helps too that skulls stack up so neatly. Or perhaps it's the fact that skulls represent a one-to-one ratio of bones to corpses, while a given human has multiple of the majority of other bones (and the most visible exception, the spine, takes up a lot more room per victim).
It's also what you're left with when you take heads as trophies and leave the rest on the battlefield. Whatever the case, when warlords and writers want to evoke terror, they create gargantuan piles of Nothing But Skulls. And stand on them. It's an old trope, but still effective.
After reading this page, skull will no longer sound like a word.
Rurouni Kenshin: Hell is depicted as full of mountains of skulls; during Kenshin's Heroic BSOD, he imagines himself there as Shishio taunts him.
Shishio, Yumi, and Hoji are also depicted in this Hell shortly after their deaths, quite cheerful about it and setting off to conquer the place. This sequence is notably the only supernatural event in the series that cannot be put down to either 'Watsuki physics' or somebody hallucinating, because there's nobody to hallucinate; it's just the omniscient audience's perspective of these guys hanging out among the skulls.
Smax: In Alan Moore's Top 10 spinoff miniseries, the lair to the den of the Dragon Morningbright is paved entirely with the skulls of children.
In the Harry Potter fanfic HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH, Harry goes to Surf Ninja Moon X and hides in a castle "which had been many skulls arranged to resemble one large one. It had been poorly done, with the cheeks fading into an amateurishly executed jaw line."
In The Return of the King Aragorn, Gimli and Legolas are nearly buried under an avalanche of Nothing But Skulls. The writers comment on this, explaining that there were different rooms for each bone, and if Aragon, Legolas, and Gimli had been in a different part of the cave they would have been buried under a pile of femurs, or kneecaps, or something.
The catacombs under Venice in Indiana Jones and the Last Crusade had niches in the walls that contained only skulls, one to a niche. Justified in that the skull is the "densest" indicator of death, those niches were probably high-density tombs and crypts. The body may not reside there, but the skull and the soul are there.
Predator; In somewhat of a subversion, goes for nothing but skulls with the spinal cord still intact. Presumably they go for more on Ebay.
Terminator 2: Judgment Day: The opening 'Future War' segment features an apparent carpet of Nothing But Skulls, seemingly specifically so Skynet's mecha can symbolically crush them beneath their feet and treads as they engage Resistance troops in yet another bitter firefight. A Shout-Out to this can be found in the losing cinematics of Wing Commander III, with a Kilrathi foot in combat armor doing the crushing.
Ghostbusters II, at least in terms of imagery. Viggo the Carpathian says, "On a mountain of skulls, in a castle of pain, I sat on a throne of blood." Also a Badass Boast or whatever.
In the opening scene of Muppet Treasure Island, there's a cavern full of skulls. They sing a line of "Shiver My Timbers".
''The Apotheosis of War''◊ by 19th century Russian painter V. Vereshchagin is a marvelous example of this trope. The fact that the artist was born in a town called Cherepovets ("Skulltown" in Russian), which was named after an ancient pagan shrine, adds to the Rule of Cool.
Parodied in Interesting Times when Cohen and his Silver Horde learn from a local that the claiming of the throne of the Agatean Empire is traditionally accompanied with "seas of blood" and/or "a mountain of skulls". The Horde eagerly begins quizzing exactly how many skulls this precisely means, and their informant gets testy: "I don't know how big a mountain! A lot of skulls!"
In The Last Hero, mention is also made of the now retired Pamdar the Witch Queen.
"She runs a shop now. Pam's Pantry. Makes marmalade."
"What? But she used to queen it on a throne atop a pile of skulls!"
"I didn't say it was very good marmalade."
In Hogfather, the Tooth Fairy has a mountain of teeth.
In Night Watch, it's mentioned that the Temple of Small Gods sorts the bodies of the dead by what bone they are. The entrance of the tomb holds the skulls.
A bit of the Star Wars Expanded Universe mentions an artist who depicted Emperor Palpatine as sitting on a throne atop a mountain of skulls. He was executed.
Gaunt's Ghosts, Blood Pact: A rumor circulates about a valley filled with millions of dusty skulls with the tops sawn off. To the point that it scares the crap out of hardened veterans of several wars, and even freaks out Gaunt himself a bit. Of course it helps that the entirety of the building they're camped in is thoroughly evil.
In The Night Angel Trilogy, there's a bridge in Khaliras made entirely out of skulls and magic. The only real point of the skulls is to intimidate and show where the bridge actually is (it's possible to cross it with the skulls gone). Did I mention this bridge crosses what appears to be a mile wide bottomless chasm, and is the only way into the castle?
Live Action TV
In the MST3K episode "Cave Dwellers" there's a giant snake pit with lots and lots of skulls. "Oh look, anal-retentive snakes, they lined up the skulls!"
More recently, we have "The Wedding of River Song", which featured a crypt full of living skulls, leftovers from the process of creating Headless Monks.
True to the band, the Metallica pinball game has lots of scary-looking skulls all over the place.
In Haunted House, most of the remains seen consist of nothing but various skulls.
Warhammer 40,000: The skull is a very common motif in this game, particularly the in the Imperium, which more often than not uses representations of skulls rather than the real thing. Chaos forces uses this motif somewhat less (for the most part), although they will use actual skulls more often.
"Skulls for the Skull Throne!"
Chaos worshippers like building altars out of them or wearing them on trophy racks, while the Imperium has flying skull-robots and buildings with skulls of the dead in shrines on the walls.
The Space Marines' Power Armor is usually decorated with skulls made of solid gold, and occasionally real skulls as well.
One of the most recognizable emblems of the Imperium is a skull. Sometimes with wings.
And a Chaos Titan is once depicted with a necklace of skulls. Providing how humongous the thing is you could guess how many skulls that would take.
Skulltaker, one of the Blood God's more dangerous servants, wears a cloak◊ made of the skulls of his fallen opponents. His table top miniature has no less than 137 skulls modeled on it.
This is a classic basing technique to make power-armored Khorne Lords stand out from the rank-and-file. Simply clip skulls off of Chaos trophy racks, arrange in a pile, and mount a miniature on top.
The Orkz are fond of taking skulls as trophies, much like the followers of Khorne. Expect to see at least one skull decorating a Warboss and-or his entourage.
As are the Dark Eldar. The special character Kheradruakh theDecapitator has thousands of skulls from various races lining the walls of his lair, all positioned carefully so their gaze converges on a central point where he sits. Creepy.
This is a common dig or in-joke on certain forums regarding certain models in the overall Games Workshop range gaining more and more skulls. Case in point...
The aptly named Khorne Lord of Skulls model has so many skulls on it that according to an interview in White Dwarf, the sculptor lost count somewhere after 200. It has several different components that, in-universe, are basically metal frames used to hold skulls in place.
The Dungeons & DragonsGreyhawk campaign setting features the Empire of Iuz. The capital city's main road is paved with skulls of Iuz's enemies. It stretches for over a hundred miles to the north of the capital, to the first petty fief Iuz took over. It's also being expanded towards the southeast to the city of Molag, more than doubling its length.
The Greyhawk cosmology/Planescape campaign features (or once featured) the Pillar of Skulls on Baator, composed of the skulls of those who hid knowledge from another, and as a result the person they hid it from died.
Heroes of Might and Magic: In one version, the Necromancer city can build a 'Pyramid of Skulls', which looks somewhat garish, but boosts your weekly production of Skeletons significantly.
Myth: The Myrkridia, horrible lycanthropic monsters from Bungie's series of games, make the skulls of their victims into platforms that rise thirty feet high and then are adorned with the Myrkridian standard. The precision with which the skulls are fitted is said to be maddening to behold.
In StarCraft, the Zerg victory results screen shows a Hydralisk atop a pile of skulls.
World of Warcraft: In several locations such as war zones or Scourge installations, there are usually many skulls strewn about. Others bones are also visible but but skulls outnumber them all. Some good old pile of skulls can also be found around ritual circles and similar locations.
Castlevania: Symphony of the Night: There are two rooms in in which the floor is made entirely of skulls, and there are huge piles of them in the background. The boss fought in this room is a giant floating ball of corpses that was hiding in said skulls before you entered, and in the upside-down castle version of that room, you face Galamoth.
Castlevania: Harmony of Dissonance: Almost the entire Skeleton Den area, which is just an immense catacombs. With, appropriately, lots of skulls used as a building material (along with other bones and non-bone materials).
Castlevania: Order of Ecclesia: The Skeleton Cave. According to the game, the bony fiends themselves created this unholy place by ransacking a nearby cementery and using the bones to built this temple of the dead.
In Sid Meier’s Alpha Centauri, there are Secret Projects playing the same role as Wonders do in Civilization. The cinematic for one of them, "Dream Twister", involves (among other nasty things) a photo of a pile of skulls.
Brutal Legend has a mountain of skulls as the first level of the game.
Sluggy Freelance: Almost used — the Mountain of Bones that the Demon King's abode sits atop is made up of all sorts of bones, but about half of them seem to be skulls, which is subject to many of the same comments as Nothing But.
The Secret Saturdays: used in episode "Where Lies the Engulfer", where a cryptid made of water smashed Doyle down to the bottom of the lake and he sees a skull leering back at him amidst a floor of bones. "Ahhh. Now that's just sick!"
In the Teenage Mutant Ninja Turtles episode "The Trouble With Augie", Donatello eventually founds a mass grave organized in this manner. While one can see bits and pieces of other types of bones, skulls are by far the most common.
Buffalo skulls were high in phosphorus and were bought up by fertilizer and explosive factories. They were piled in a giant mound before being shipped off.
Skull Tower of Niš. A tower made of the skulls (of the Serb soldiers defeated in a battle that was fought near the place during a major uprising) and stone blocks by Turkish commanders to discourage Serbs from another revolution.
By the way, discouragement? It failed. Serbs rose again couple years after that, and actually got to be represented by one of their own.
The tower is now a national monument. Also the rebels weren't just defeated, they blew themselves and many of the Turks up.
The Aztecs and their neighbours routinely displayed skulls on special racks
Assyrian armies piled up pyramids of skulls.
The Mongols were also quite fond of this as a form of psychological warfare. Timur reputedly built a pyramid out of 90,000 skulls outside of the city of Dehli to coax the city's surrender.
Catacombs and ossuaries (where bones are taken after they've been in a grave for a respectable amount of time to free up graveyard space), they're stored by bone type and size, not by owner, because it's a more efficient use of space.
In the Paris Catacombs, while there are all kinds of bones, skulls are carefully set in front of the piles to keep them from collapsing, or just for making fun shapes (there's a pattern of skulls in shape of a heart for example in one bone-pile.) The quick impression of the place comes close to the trope, even though careful scrutiny quickly proves it false.
In Portugal, the Chapel of Bones has wall decorated with nothing but skulls.
Memorials and museums for the Rwandan Genocide have... very neat stacks of skulls. A hell of a lot of them. There are a few reasons for this, the first being of course that skulls are small, easily stackable, and represent one clear death each, thus having a huge emotional impact. The second being that the large scale systematic mutilation of the victims and use of explosives in small confined areas (like churches) left it rather difficult to determine which bone belonged to whom, and it would be impossible to piece together every one of the thousands of skeletons.
Pol Pot is famed for his love of this trope. The Tuol Sleng Genocide Museum has shelves of the skulls of his victims.
Which The Onion then played with by saying that Cambodia was planning to switch to a skull-based economy, "which will be a fantastic boom to the world economy once they actually produce any good or provide services."
This◊ political cartoon of United States President Zachary Taylor, or possibly General Winfield Scott (it's debated). At any rate the cartoon is an attack on the Whig Party, the skulls and sword referring to the Mexican American War in which both Taylor and Scott fought, and the "one qualification" being bloodthirstiness.