Arc Symbol

The symbolic equivalent of Arc Words or an Arc Number. A picture or symbol appears multiple times and places over the course of a Story Arc. No explanation is given for the symbol until well after the eagle-eyed fans have noticed it and started debating its meaning. These often either serve as Foreshadowing, or tie into the theme of the story.

Note that this is distinct from Sigil Spam, which is about organizations who put their symbol on everything they possibly can. But it is possible for the two tropes to overlap: If a symbol that has been appearing everywhere since the first episode is revealed in the season finale to be the symbol of the Ancient Conspiracy that secretly rules the world, then it's an Arc Symbol and Sigil Spam.

Anime and Manga

 * Ghost in The Shell Stand Alone Complex has the Laughing Man Symbol.
 * The Eye of Wdjat symbol (not quite the Eye of Horus) on Yu-gi-oh. Appears on all the Millenium Items except the Key, and on people's foreheads when they are wielding or being controlled by the Items' magic. It also crops up on artifacts that are connected to the secret of the Pharaoh's past. It is Defictionalized in a couple of the cards, where it is finally named.
 * SEELE's logo is a mix of Sigil Spam and this trope. It turns out that their logo is the face of Lilith, the Second Angel.
 * Gurren Lagann. Spirals. That is all.
 * Uzumaki has spirals in a way entirely dissimilar to the above.
 * The seemingly omnipresent penguin-head logo in Mawaru Penguindrum, which appears on several objects such as a Kanba's backpack, the back of a skunk, and.
 * Episode 26 of Yu-Gi-Oh Ze Xal introduces new main antagonists known as the Tron Family who possess "crests" on parts of their bodies. Thirty episodes later, we still don't know what the heck their symbols mean!

Comic Books

 * The bloodstained smiley face and doomsday clock in Watchmen.
 * In 52, the number 52 itself is used constantly as references to the main plot. It's an Arc Number, but also symbols and concepts associated with 52 (such as card decks) are used.
 * The Sigil in Cross Gen comics' Myth Arc.

Film

 * The kingdom's sun insignia in Tangled.
 * The standard of two snake heads facing each other in The Movie of Conan the Barbarian.
 * The Natural has lightning. It splits the tree open at the beginning of the film, is carved into the bat "Wonderboy," strikes before Roy knocks the cover off the ball in his first at bat, appears on a patch that the Knights wear, and again strikes before

Literature

 * Keith Roberts' Pavane stories, later assembled into a novel, are all linked by a symbol (designed, of course, by Roberts, who was an artist as well as an author). The symbol depicts two pairs of arrows, one converging and one diverging, within a circle.
 * Mark S. Geston's Lords of the Starship has frequent mentions (though no depictions) of a mailed fist and pegasus insignia worn by various enigmatic characters who drive the plot over the course of a century and a half.
 * The Wheel of Time series has a lot, including the Dragon's Fang and the Flame of Tar Valon.
 * The dwarf rune of The Summoning Dark in Thud.
 * Harry Potter: The line-in-a-circle-in-a-triangle symbol recurs in the last book, as it symbolizes the Deathly Hallows.
 * Which is not really an Arc Symbol, until you remember that it is mentioned once in the previous book.
 * The Trystero post horn in The Crying of Lot 49.
 * Brave Story boasts a star-shaped sigil which is found on various locations all over the world of Vision -- which, when used in harmony with a certain magical mirror, creates a portal between Vision and the real world.
 * The Hunger Games has Katniss' mockingjay pin, which becomes a symbol of La Résistance and serves as the cover for the first book.
 * Clear Light of Day, by Anita Desai, has hands EVERYWHERE.

Live Action TV

 * The Dharma logo in Lost
 * Heroes has the eclipse, everything from a real one to an illustration by Isaac. Another is the RNA symbol, a single helix with half of some base pairs coming off of it. This is also used as the symbol for Takezo Kensei, as it is stated to be the characters for "god send".
 * The Blue Sun logo in Firefly was going to be this until the series was so rudely interrupted.
 * The Cracks in the Universe in series 5 of the revived Doctor Who appear at least Once an Episode.
 * The Eye of Rambaldi in Alias.
 * The tattoos in Twin Peaks.
 * The yellow umbrella in How I Met Your Mother is a subversion -- we already know that the umbrella signifies the mother, but Ted doesn't.
 * Purple clothing for Ted, Marshall, and Lily (and very much not Barney and Robin) is an inexplicable trend in season 7 -- and as of "Tick, Tick, Tick", is definitely not a coincidence -- but the significance has not been revealed yet.
 * The infamous Ducky Tie. The audience knows that Barney will wear the ducky tie again before season 7 ends, he put on the ducky tie right after getting together with Nora and took it off, and a flashforward to his wedding show him having a conversation about ties with Ted that is obviously really a conversation about his love interests.

Toys

 * The Three Virtues of Bionicle
 * Eventually revealed to be.

Video Games

 * The reversed peace sign in Deadly Premonition. It's actually
 * The symbol of the vault in Borderlands.
 * The stone knife in Echo Bazaar, particularly in the "What the Thunder Said" storyline.
 * The eye of the Goddess in Albion, arguably.
 * Potatoes in Portal 2.
 * The Yatagarasu logo in Ace Attorney Investigations.
 * The bulldog logo crops up very often in Mirrors Edge, until Faith discovers that it belongs to, one of the conspirators in Project Icarus.
 * The One-winged Eagle in Umineko no Naku Koro Ni.
 * The Tanooki tail is a recurring feature in Super Mario 3D Land.
 * In Mass Effect, the Citadel's council chambers and the Serpent Nebula, where the Citadel is located, are
 * Chains in Bio Shock. Andrew Ryan's objectivism is professed as "the great chain," and there are many decorative chains in the architecture of Rapture
 * Chains also figure heavily in Dragon Age II in keeping with some of the themes of the game (the meaning of slavery and freedom; certainty versus free will) and Kirkwall's long history as a center of the slave trade. As Fenris reminds Anders, "No one is truly free."
 * Hysteria Project has the mysterious H-emblazoned maze tattooed on the protagonist's arm.
 * The Blood Dragon in Dragon Age, as seen everywhere from the game box to the game over screen.
 * The Symbol of Torment in Planescape Torment, tattooed on the nameless hero's arm.

Webcomics

 * Gunnerkrigg Court has a sigil of an eye with a line through it. It shows up on the walls of containment cells, on spirit-binding magic, and on a necklace worn by a character's mother. It's eventually revealed that the spirit-binding magic was actually a union of magic and computing, and the other occurrences of the symbol are remote interfaces for accessing the magic computer. Also alchemical symbols -- Antimony for, well, Antimony Carver, Mercury for Renard the Fox (or rather, for his body-snatching ability--both it and the symbol were associated with Coyote in the backstory), Lead for the Court's Protector and great Sigil Spam of Bismuth for the Court itself.
 * Superego has the circle and all its variations, representing each of ten protagonists and their.
 * Bequerel's face in Homestuck.
 * Homestuck has been getting full of these, but increasingly common is the "broken record" symbol, symbolizing, as well as various other themes related to breaking and repeating things. Homestuck walks a fine line between Arc Symbols and Sigil Spam.

Web Original

 * The Operator Symbol from Marble Hornets, or The Slender Man Mythos in general.
 * The yeti symbol in Alice and Kev.
 * The yellow sign with the (/) symbol over a heart with a cat and bunny in There She Is!
 * In the Evillious Chronicles (a series of Vocaloid music videos and novels by Mothy), a symbol that frequently comes up is flowers, to symbolize corruption and sin. Notable examples are in Duke Sateriajis Venomania (commits the sin of Lust in "Duke Venomania's Madness", represented by a flower), Princess Rilianne Lucifen D'Autriche (referred to as an 'evil flower' in "Daughter of Evil", and Mikulia Greonio (the title of her feature song, and her nickname in said song, is "Flower Of The Plateau"). Also, gears are something of a symbol for the Clockwork Lullaby series.

Western Animation

 * In Avatar: The Last Airbender, the Order of the White Lotus secret society inconspicuously integrates their symbol into their surroundings, to denote a friendly place.
 * Images of lion-turtles also appear in several places before a real lion-turtle provides Aang with information about the Deus Ex Machina ability he uses in the finale.