Vanquishing evil is actually pretty easy: just grab a Chosen One, give them a sword (or just a herring — Chosen Ones are a very resourceful lot), point them in the right direction and just wait until the evil empire falls. In fact, the only challenge in this puzzle is figuring out just who and where the Chosen One is in the first place. You don't want to end up with a Fake Ultimate Hero, after all.
Well, worry no more!
For your convenience, the gods were nice enough to physically label your Chosen One in some way. Typically, this comes in the form of an unusually shaped birthmark or strange hair/eye color. For bonus points, there will often be a vague allusion to this mark or phenotype that will only make sense once the Chosen One actually appears.
A subtrope of Distinguishing Mark
Kinnikuman has the Kinniku family birthmark on his buttock. He presents it in the Scramble For The Throne arc to prove that he's the rightful heir, only for the impostor princes to reveal their own birthmarks on their backs.
The Signers from Yu-Gi-Oh! 5Ds have the Dragon's Birthmarks, signifying that they were chosen by the Crimson Dragon.
The protagonist of the French-language series, Le Scorpion has a scorpion-shaped mark on his back, from which he derives his name. Because of this mark, some people consider him to be the Devil's son. It turns out to be a scar caused by being thrown against a red hot metal scorpion as an infant by Tribalidi, whom the Scorpion and the reader had been misled to believe is his father.
The Fifth Element - The eponymous Fifth Element, Leeloo, has the symbols for the four elements on her wrist.
Willow - The movie introduction details this trope, exactly, right off the bat.
The Court Jester - The Rightful Heir (still an infant) has a birthmark on his butt. There are a couple of scenes of Hawkins holding the infant in his arms, lowering the swaddling clothes just far enough to reveal the birthmark.
Subverted in The Golden Voyage of Sinbad, when Ms. Fanservice's eye tattoo is seen by the savage tribe. The Plucky Comic Relief guesses that they're so excited because they think it's a Birthmark of Destiny that brands her their goddess, but the character who knows their language reveals that, no, it's actually a sign she should be given to the local one-eyed monster. (A cyclops/centaur, that is.)
In The Dreamers, Theo and Isabelle are twins and share the same birthmark.
In Cloud Atlas, each protagonist of the six stories has the same comet-shaped birthmark. (in the book, the one for the sixth isn't Zachry, but his love interest)
The Giver: A spot-shaped birthmark appears on the wrists those who can "see beyond." This was changed from Occult Blue Eyes in the novels.
In the Discworld series, Carrot casually mentions having a crown-shaped birthmark, which marks him as the rightful heir of the Ankh-Morpork throne.
Invoked in Wyrd Sisters, when the witches talk about a "strawberry birthmark", despite there being no evidence the lost heir does have one. And nobody's entirely sure what it even means; Nanny Ogg seems to vaguely think it would taste of strawberries.
In Guards! Guards! the characters discuss birthmarks as if they're something that can be handed down from father to son.
One of the Jedi Apprentice books had this, only the birthmark would only appear in a certain chamber. This revealed that the Crown Prince was not actually the rightful heir, instead the heir was the king's daughter from a previous marriage to a commoner. Who also happened to be the leader of La Résistance.
Morgon in Patricia McKillip's Riddle Master trilogy has three star-shaped birthmarks on his forehead.
Deyna's birthmark in The Taggerung. It's a flower-shaped mark on his pawpad, foretold by a seer to mark him as the titular Taggerung (a creature destined to become an unstoppable warrior). This allows the villains to know they've got the right baby when they kitnap him for the honor and strength of their clan. After his relatively effortless Heel Face Turn and the resulting fighting, Deyna has this mark tattooed over so his paw looks like any other otter's paw.
In The Outlaw of Torn by Edgar Rice Burroughs, Norman of Torn has a lily-shaped birthmark on his right breast, which eventually proves that he's Prince Richard, lost heir to Henry III.
The royal family in the Hero Series all have a royal birthmark indicating as such.
In The Prophecy of the Stones, the gift of hope, which allows the protagonists to defeat evil, has been passed down through the generations, with the carriers of hope bearing a sun-shaped scar on their palm. The other protagonist, Joa, reveals at the end that she has such a scar, which connects her plotline to the main one.
In The Belgariad, Garion has a discoloured mark in the shape of a circle on one of his palms. This mark is actually possessed by every descendant of Riva who is in line to inherit the Rivan throne.
Sorcerers also have such a mark somewhere. Polgara's is in her hair.
Among the Ulgo people, the one destined to become their holy man is known by the colour of his eyes at birth.
In Joanne Bertin's Dragonlord books, were-dragons are born as humans who have various birthmarks, which can be anything - albinism, splotches of color, shortness, webbed fingers, etc. These are called their Marking. Some of these run in families and the vast majority of birthmarked humans aren't nascent Dragonlords, but oddly enough there is still a stigma to having a birthmark.
Live Action Television
On the original Doctor Who, Turlough's long-lost little brother was believed to be the Chosen One by his adoptive people, due to a distinctive mark on his shoulder. Subverted in that it wasn't a birthmark or a mark of Destiny, but an identification brand placed on political prisoners by the ones who'd exiled both brothers.
In The Mystic Knights of Tir Na Nóg, the druid Cathbad believed Rohan was The Chosen One because of the Mark of Destiny he found on the baby boy. Rohan quickly realizes his destiny when the quest to find the legendary hero Draganta ends with the reveal that he is Draganta. At the end of the first (and only) season, Rohan discovers to his initial horror that the Mark of Destiny is actually a birthmark shared by the other members of his biological family his half-brother Lugad, the half-demon Warrior of Temra, and their mother Queen Maeve.
In Storm Of The Century, the protagonist Mike's son Ralphie has a little brown spot on his nose that his parents call a "fairy saddle". Andre Linoge immediately wins over Ralphie by calling it a fairy saddle too. It's implied near the end that Linoge rigged the random lottery to decide which child he would take as his own so that he could have Ralphie because of the fairy saddle.
In Anna Russell's "How to Write Your Own Gilbert and Sullivan Opera," the fat contralto character of Dandelion reveals (in song, assisted by chorus) that the rich tycoon Claude Billy Bunion was born with a mark "just like a Spanish onion" behind his ear, but being a stupid Gilbert and Sullivan character she switched the bassinets. Such a mark is discovered on the tenor, whom the soprano can now marry instead of the patter baritone, who has to marry the contralto.
Parodied in the BBC radio series Hordes Of The Things, where Prince Veganin is told that he bears the birthmark of the High Priest of Zylbor (just after he's slain the old one). Turns out that he's not the only one with the mark, however: the Priests are collecting birthmarks from every possible claimant and throwing away the rest of their bodies, on the assumption that they'll be able to fit all the pieces with birthmarks together into their new High Priest one day.
Certain incarnations of Link from The Legend of Zelda have a birthmark in the shape of the Triforce on their left hand. Occasionally happens to Zelda herself, though not as often.
The Branded from Path of Radiance and Radiant Dawn each have a mark somewhere on their bodies to identify that they are descended from both beorc and laguz. A particular brand on the back of someone's right hand marks the bearer as a descendent of Lehran and the true apostle.
Rocky and Bullwinkle: Bullwinkle has one of these on on the bottom of his foot/hoof. It's subverted at the end when it turns out that it's actually the design on his bathroom floor mat, imprinted when he stepped out of the tub.
And double-subverted when he later reveals that he has another one on the sole of his other foot that won't wash off.
Teen Titans gives Raven glowing red birthmarks in the shape of occult-looking symbols all over her body as a sign that she is the daughter of/portal for the demon Trigon. However, these marks are normally invisible and only appear when Trigon is stirring (i.e. only when they're relevant to the plot).
Subverted in an episode of Sagwa, the Chinese Siamese Cat where Sagwa's younger sister Sheegwa is thought to be a princess because of a star-shaped birthmark on her body, but at the end of the episode the "birthmark" is accidentally washed off and is revealed to be just a stain of mud.
In the season 4 premiere of My Little Pony: Friendship Is Magic, Twilight Sparkle's Cutie Mark gains new meaning as a true mark of destiny, as her six-pointed star cutie mark matches both the (retconned) past shape of the Element of Magic, as well as a the symbol on the Tree of Harmony. The Expanded Universe book The Journal of the Two Sisters confirms this further, as when they saw their cutie marks on the Tree of Harmony, they predicted that there would be a third pony with a third symbol, a six-pointed star. This was likely intended from the get-go thanks to Fridge Brilliance, but it doesn't gain any confirmed meaning until a few seasons in.