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Anime & Manga
- In the Yu-Gi-Oh! episode where Joey is forced to wear a dog suit, he actually holds a sign with a question mark on it when he's confused about Dungeon Dice Monster's rules.
- Hanaukyō Maid Tai:
- Episode 9. Konoe Tsurugi refuses to have her picture taken because she doesn't want the camera to steal her soul. When she hears this, Mariel has three question marks appear next to her head, one at a time.
- Episode 11. When Ryuuka asks Taro if he's interested in someone else, he looks at Mariel. Mariel then has question marks to each side of her head. Later, when Ryuuka appears before Taro in his bath a question mark appears over his head.
- Episode 12. Ryuuka has just given Taro a giant cake shaped like her for his birthday. When she sees him staring at it, a question mark appears over her head.
- Episode 15. Taro has a question mark appear above his head several times when he's puzzled.
- One Piece: Used by the Gorgon sisters and Luffy when they find out the latter is immune to Hancock's petrification powers.
- Chess notation marks bad moves with one question mark, blunders (very bad moves) with two.
- Peanuts uses the "'?' in speech bubble" variety.
- Beetle Bailey. General Halftrack sometimes has a question mark appear over his head when he comes upon members of his staff acting in a bizarre manner.
- All ''Popeye comic strip artists have used this, but none so more than Bud Sagendorf, who downright littered his strips with question marks. A panel with question marks in four or five individual speech bubbles were hardly unusual.
- The Phantom and Mandrake The Magician uses a lot of question marks in indvidual speech bubbles. It's probably no coincidence that both strips were created and written by Lee Falk.
Films — Animation
- Done in The Colour of Magic to represent that the tourist Twoflower doesn't understand what the Ankh-Morporkeans are saying.
- Not sure if the scene from Lost where Eko goes to the other hatch counts. There's a giant "?" on the ground.
- Psychedelic band ? and the Mysterians.
- Many Role-Playing Games indicate Confusion status with question marks.
- In the Pokémon Stadium games, question marks appeared above a confused Pokémon's head. In other games, it is usually portrayed by birds flying around its head.
- In Pokémon Red and Blue, the confusion status effect was indicated by two question marks appearing above the Pokémon's head, each accompanied by a sound effect suggesting the "huh?" sound.
- Also, question marks appear above a Pokémon's head when it uses Nasty Plot.
- The protagonists of Persona 3 and Persona 4 do this to indicate confusion.
- In Psychonauts, the icon for the "confusion" power depicts a perplexed head surrounded by question marks, and the confusion projectile itself looks like a giant question mark that the protagonist throws at the enemy, after pulling off the dot like a grenade pin.
- Disgaea has no confusion status effect, but it uses question marks to represent amnesia (the "silence" Standard Status Effect) instead.
- Nospikes from Commander Keen 6 like to charge at you, but if they run off a ledge, they stand in mid-air for a while and a question mark appears above their head before they fall.
- In Cave Story, trying to examine an object without something to examine will cause a questionmark to pop up.
- If the Elite bosses from Hero Core try to use an ability Cast From Hitpoints with only one point left, a question mark will appear above their heads.
- When a soldier in Metal Gear sees something unusual a question mark appears above their head (followed by an exclamation mark if they see you).
- In Ōkamiden, since Chibiterasu relies on his partners for exposition, any time you try to examine something without your partner, all you get is a whimper and a ? above Chibi's head.
- In Stealth Bastard, question mark appears over to robots and cameras if they detect the presence of player but haven't gotten fully alert yet.
- In Sonic the Fighters, right after Dr. Eggman zaps your character with a cloning ray (which produces a grayscale doppelganger).
- Also, the Chao sometimes turn the floating balls atop their heads into question-marks.
- The "Use" command in Tombs & Treasure depicts a man scratching his head with one of these floating next to him.
- The standard emoticon for confusion is a colon and question mark, thustly: :?
- The trademark of the perpetually confused Blitz on The Funday Pawpet Show. A question mark was put on a stick and floated above him.
- In the Tom and Jerry cartoon Ah, Sweet Mouse-Story of Life, Jerry ends up walking off a construction beam and a question mark appears above his head just before he falls. In a Ninja Prop moment, he grabs the question mark and uses it as a hook to latch onto a ledge. Tom later attempts the same thing, but before falling he becomes shocked rather than surprised, getting an uselessly straight exclamation mark instead.
- A question mark appears above DM's head at least once in Danger Mouse.
- Felix the Cat would often pick up the question marks that form over his head and use them as tools. In at least one cartoon, his tail turns into a question mark.
- In the Classic Disney Short A Gentleman's Gentleman, as Pluto the Pup wonders how to get a gumball from a gumball machine, one of his ears forms a question mark.