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In Tengen Toppa Gurren Lagann, the logo of Team Gurren is a flaming skull with Cool Shades, bearing no small resemblance to the Gurren itself. At the end of the series, Gurren Lagann takes command of Arc Gurren Lagann takes command of Super Galactic Gurren Lagann takes command of Tengen Toppa Gurren Lagann, a Humongous Mechathe size of a galaxy, which is comprised entirely of giant flaming skulls.
This is a favorite of Gina Diggers' father, making his head appear to be on fire, as a means of intimidating would-be suitors to his daughters. (He's an archmage. It's just an illusion.) He even calls it the "magical equivalent of polishing the shotgun."
In the Doctor Who Magazine comic story "Hunters of the Burning Stone", the titular villains' heads appear to be flaming skulls. This turns out to be a Call Back to the earlier TV story mentioned below.
According to Bill Cosby, this is what happens when your wife discovers you've given the children chocolate cake for breakfast.
I've always heard about people having a conniption, but I've never seen one. You don't want to see them. My wife's face split; the skin and hair came off her face, so there was nothing except a skull! And orange light came out of her hair, and it lit all around, and fire shot from her eye sockets and began to burn my stomach, and she said: "WHERE DID YOU GET CHOCOLATE CAKE FROM?!"
Warhammer Fantasy traditionally has a Bright/Fire magic spell called "The Burning Head".
Also: Screaming Skull Catapults. The ancient Khemri empire had a habit of keeping the heads of executed criminals, coating them in a special kind of pitch that not only burned well, but made a horrific screaming sound, and firing the things en masse at opposing armies via catapult. Coming back as a race of skeletal undead has not cured them of this habit.
There's an upgrade for the catapult that lets you fire the skulls of the specific race being fought at them. This hurts their morale rather badly.
Khornate daemons in Warhammer 40,000 are occsionally armed with the dreaded Burning Brass Skulls of Khorne. Presumably they kill people by being f*** ing metal.
So who gets to wield the Burning Brass Balls of Khorne?
Biker Nob Gutsmek once destroyed a Titan by ramping into it and killing everybody onboard. The crew's skulls, kept as trophies, are still on fire.
A feat called "Spell Theatrics" lets a caster change the visual effects of a spell. The example given is making a Fireball into a flaming skull. There are several types of undead that also take this form.
In adventure G3 Hall of the Fire Giant King, King Snurre's symbol is a flaming skull.
The Yu-Gi-Oh! card game has a card actually called Burning Skull Head, as well as Skull Flame and Supersonic Skull Flame. Fittingly, Burning Skull Head and Skull Flame are FIRE-attribute Zombies (Supersonic Skull Flame is WIND instead).
The Legend of Zelda series has Bubbles, flaming skulls which flutter around on little bat wings. Less awesome and more annoying in this case, as they seal Link's ability to draw his sword. However, that was absent all together in games after Wind Waker, and would just either freeze or burn Link.
Lost Souls in the Doom series are pretty much Bubbles, only more lethal than annoying.
In Strong Bad's Cool Game for Attractive People Episode 2: Strong Badia the Free, the Drive-Thru Whale prompts Strong Bad to set a pile of papier-mache skulls on fire with the hint "would you like flaming skulls with that?" Strong Bad, being Strong Bad, replies "You have to ask?"
Prometheus from Mega Man ZX could summon 4 of these as one of his attacks.
One of the numerous varieties of Goddamned Bats of Terraria is one of these, and can usually be found in dungeon areas.
Variants of these appear as standard enemies in some dungeons throughout the Golden Sun series.
Flaming skulls are a destroyable hazard in Samurai Warriors 3 in its Murasame Castle Mode stages.
RuneScape has wearable flaming skulls as a reward for redeeming a specific subscription card from specific stores within a certain time period. Sadly it is cosmetic only and gives players no advantages; it does look awesome though.