A character's eye has great supernatural power. Usually, the eye grants the user power over perception, either the target's (illusion, mind control) or the user's (telepathy, premonitions, clairvoyance, etc). In most cases, direct eye contact or at the very least line-of-sight is required. Other restrictions may apply.
If only one eye has magical abilities, an Eyepatch of Power is very likely, especially if this eye possesses a distinct look, like color or shape (which might only appear during active use). The Magical Eye is often used as an excuse to apply certain patterns or symbols to a particular power, therefore making it Cool and Symbolic. Even more symbolic, the eye possessing the power is almost always the character's left eye (the left eye is considered the "sinister" eye, as "sinister" was once a word for "left"). Closely related to the Red Right Hand.
Magical eyes can be any color, but are usually glowing unusual colors like Red Eyes, Take Warning or two colors at once.
See also Eye Beams for a more directly offensive use of eyes. If the magical eye can cause hypnosis, its a Hypnotic Eye. Do not confuse with Faceless Eye or the more mundane Death Glare. Compare Excessive Evil Eyeshadow. The technological equivalent is an Electronic Eye. No relation to Magic Eye, that autostereogram thing where if you look at it just right, you can see a cat or a dolphin or whatever.
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Lelouch of Code Geass possesses a "Geass" in one eye that allows him to compel absolute obedience to his commands. Requires direct eye contact (can be blocked by visors or bounced off mirrors) and can only be used once per person. Other characters in the series have magical eyes that let them read minds, paralyze people, see the future, rewrite memories, steal bodies...
Later on, Jeremiah Gottwald gets an "anti-Geass" that allows him to cancel the effects of ANY Geass in a certain radius. It even looks like an inverted version of the standard Magic Eye.
Pegasus of Yu-Gi-Oh! was given the Millennium Eye, previously owned 3,000 years ago by the Turn Coat Akunadin. It granted him the power to read minds, steal souls and (like the other Millennium Items) probably possessed other sinister powers if one knew how to tap into them.
In Death Note, characters with a Death Note could make a deal with Shinigami haunting the book — granting them Shinigami Eyes, which have the ability to know both the true name and the date of death of anyone whose face they can see. This makes it much easier to kill using the note — and all for the low, low price of half of one's remaining lifespan. Several characters made the trade, but Light steadfastly refused, trusting his skills as The Chessmaster to see him through.
Fuhrer King Bradley in Fullmetal Alchemist possesses the "Ultimate Eye". This is his left eye, which holds his Ouroboros that gives him the foresight to see all possible outcomes of a given situation, allowing him to predict the moves of any opponent before they happen. His original eye rotted out when he was turned into a Homunculus and is covered by an Eyepatch of Power.
Soul Eater has an immortal werewolf named Free who stole Mabaa's eye and replaced one of his own with it, granting him the ability to use spatial magic.
Hiei of Yu Yu Hakusho had a "jagan" (lit. "evil eye") eye in the middle of his forehead, which bestows vaguely-defined psychic powers and a huge power boost when activated. His Eyepatch of Power came in headband form.
In what might be a case of Early Installment Weirdness, as it only happened once near the start of the series and in a movie of questionable canonicality, he can also turn green and sprout more Jagan-lookalikes all over his body to amplify its power.
A couple exist in Naruto: the Sharingan, the Byakugan, and the Rinnegan.
The Sharingan grants the user enhanced vision, eidetic memory, and the ability to perceive chakra patterns. The upgraded form, the Mangekyo Sharingan, is unlocked by killing one's best friend and grants the user Story Breaker Power in the forms of Amatersau, black flames that cannot be quenched by conventional means, Susano'o, a nigh-invincible spectral armor, and Tsukuyomi, an unbreakable illusion technique. The only person to wear an Eyepatch of Power, Kakashi, has one of these, as his Sharingan is constantly active and depletes his chakra supply rapidly when uncovered. Some of the Sharingan's other tricks are varied upon the user and very extravagant, such as Kamui, which can send the victim into another dimension.
The Byakugan gives three-hundred-fifty-nine-degree x-ray vision, allowing the user to perceive everything around him and see chakra points on a ninja and strike accordingly. The Byakugan has a blind spot that can be exploited, but doing so requires massive amounts of skill.
The Rinnegan is a Superpower Lottery, but its primary feature is the Captain Pl... er, ability to use all five elemental chakras, as well as absorb chakra virtually at will.
Orochimaru can project his Killing Intent specially well though eye contact, which can paralyze his enemies, if they're not strong enough to resist it. Probably that's why it is never seen again after its initial use.
Mido Ban of Get Backers inherited his jagan (see above) from his grandmother. If he makes direct eye contact with someone, he can induce a hallucination (most often in the form of Mind Rape) that lasts for exactly one minute of real-world time. Limited by the fact that he can only use it three times a day, once per person per day.
In Rurouni Kenshin, the man-slayer Udô Jin-e uses a sword style that possesses a technique unique to it known as Shin no Ippô, in which he uses his ki to immobilize people with a glance of his eyes. He can even use his Blade Reflection to perform the Hyoki no Jutsu, in which he hypnotises himself to bring out his full strength.
Dominique the Cyclops from Trigun has a demonic-looking eye, complete with snake pupil, behind a mechanical eyepatch/shutter that allows her to distill her opponent's senses.
Lord Darcia in Wolf's Rain is cursed with a yellow wolf's eye (his left) which can render people unconscious. Usually covered by a mask. After he attempts to enter paradise and is destroyed, his yellow eye is all that's left of him. While the world's ecology is regenerated by the lunar flowers, his eye turns some of them black, tainting the world with its evil.
Sven Vollfied's Vision Eye in Black Cat has the power to see a few seconds in the future, although this is apparently severely fatiguing. It later upgrades into the less energy consuming "Grasper Eye" that slows down what he looks at, enabling him feats like avoiding bullets fired at him (though from the point of vue of the others, he seems to be the one whose movements are being accelerated).
In Gundam 00, Allelujah Haptism has a greyish eye, whereas his Hallelujah persona has a brilliant yellow one. As he switches personalities, his Peek-A-Bangs flip to the other side of his face, displaying only the appropriate eye. At the end of the first season he connects to both personalities at the same time, pushing his hair out of his face and revealing both eyes at the same time.
Rokudo Mukuro of Katekyo Hitman Reborn! has a red eye with kanji as the pupil, ranging from one to six. Each kanji represents a different "state" in the Buddhist Samsara cycle of reincarnation, and gives him a different power. His spirit medium/possessed girl/Morality Pet/etc., Chrome Dokuro, wears an Eyepatch of Power on the same eye Mukuro does, and when it's removed, it's implied that he materializes through the power of illusions and takes over for her.
In Dragon Ball, General Blue has evil eyes which paralyze anyone who looks into them, glowing blue in the process. Like Medusa, but without the petrification.
Blue's powers are more akin to Psychic Powers, given that at one point he was able to tie Goku and his friends by manipulating several ropes with psychokinesis. On the other hand, he apparently needs to focus said powers thru his eyes; something which Goku took advantage of with his "JanKenPon" technique.
In Steel Ball Run, after Gyro Zeppeli gains the Saint AKA Jesus corpse's right eye, he gains X-Ray vision and the ability to see with his steel ball weapons.
And Diego gets the corpse's left eye and gains the ability to transform into a were-raptor.
Black Butler has Ciel whose right eye has a pentagram on it. The design makes his eye lighter and more of a purple color than his normal blue eye. He wears an Eyepatch of Power to cover his eye unless its power is needed. The pentagram is proof of his contract with Sebastian, his demon butler.
Wisely, one of the Noahs of D Gray Man, has three evil eyes in his forehead. In his first appearance, he makes heads explode.
Of course, let's not forget the hero whose left eye can see the souls powering Akuma.
Unsurprisingly, Kakeru, the protagonist of of 11eyes, has a golden eye that gives him precognition.
In 666 Satan are the Cyclops who have a birthmark in the middle of their forehead. This is, in fact, a closed third eye which grants them the ability to "program" movement into inanimate objects. They can make, for example, projectiles miss the Cyclops, have lying debris suddenly hurl itself at an opponent, turn about any sharp objects into deadly projectiles, etc. Shown Cyclops using this ability are: Kirin, Mei, Tsubame and Kirin's father.
The Raijin Tribe in Fairy Tail all have this ability. Evergreen has can turn you into stone, Bixlow has the ability to take people souls and put them into dolls and Fried's ability hasn't been explained yet.
Erza is another example. Her artificial eye lets her ignore illusions and such, and also lets her turn back from stone.
The hero and heroine of Basilisk both have magic eye abilities, hence the Market-Based Title of the series. The hero can turn the murderous impulses of others against them, filling them with pain and fear and driving them to suicide. The heroine's eyes give her an Anti-Magic ability that disables the powers of anyone she looks at.
In Strike Witches, Mio's right eye allows her to see the core of a Neuroi. She covers it with an eyepatch when not in battle.
A rather mundane example by comparison appears in Gamaran: According to ToujoShungaku, both Gama and his father Jinsuke have the "Eyes of Divine Sight". As he puts it, said eyes are far more keen and perceptive than those of other warriors, allowing them to "read" the opponent's body language and anticipate their moves.
Tsubame Akifuji of Cat Paradise has the "Eyes of the Symbol", which allow him see every detail of anything he observes, even the ones that normal humans couldn't see, whether he wants to or not. They also allow him to remain aware of his surroundings even while he's possessed.
In The Unlimited Hyoubu Kyousuke, Andy has an impressively (implied-to-be-) multi-tasking one. It allows him to block out others' psychic powers as well as contact via pseudo-video his boss to report on his infiltration of Kyousuke's mafia-like group, PANDRA.
The Emerald Empress & the Emerald Eye of Ekron, in Legion of Super-Heroes. In one memorable scene, she grows to giant size, tears out her own eye, and sticks the Emerald Eye in the socket.
Wildguard: Casting Call featured the literally evil eye Wandering Eye, who attempted to use his hypnosis powers to force his was onto the team. Failing that, he hypnotized to other rejected applicants and forced them to serve his agenda of enslaving the entire world to his will, allowing him to finally be somewhat accepted by society. He was accidentally killed when Exploding Girl went critical.
Tommy Monaghan from Hitman had solid black eyes (no pupil, iris, or white, just black). His powers were x-ray vision and mind-reading anyone in his line of sight (he didn't mind-read too much - it gave him migraines). This made him very difficult to sneak up on.
Richard B. Riddick, the Anti-Hero of Pitch Black and The Chronicles of Riddick has surgically-enhanced hypersensitive eyes which require him to wear special goggles during daytime. They allow him to see in the dark, and when he takes off his goggles his eyes are shown to glow.
The video game suggests his special eye powers may actually be a result of being the last surviving Furyan.
In the 2009 film Push, mind-influencing telepaths need to make eye contact with their targets. The so-called "pusher's" pupils dilate drastically when they use their powers
In Shinobi Heart Under Blade, Oboro has a technique called Hagen no Do—literally "pupil of annihilation", and also translated as "Piercing Eyes". She only uses it once. It basically let her do something to the effect of causing her foe's nervous and circulatory systems to break down and explosively hemmhorage, leaving him bloody and helpless on the ground, by just looking at him.
A widespread European folk belief was that envy physically changed the eye and caused it to inflict misfortune on those whom the person envied. Note that this was held to be out of the person's control.
Alastor "Mad-Eye" Moody of Harry Potter has a glass eye that can spin in its socket to face any direction, has x-ray vision, and can see through most illusions.
Mr. Teatime of Terry Pratchett's Discworld has a grey glass eye—which some of his associates claim is in fact a scrying crystal—that seems to give him the ability to perform such feats as moving faster than the normal human eye can see and doing backflips on thin air. Also interesting is that the other characters refer to his remaining eye as the scary one. His pinprick pupil is said to see into one's soul. If the crystal rumor is true, it might explain his Ax Craziness: Discworld magic is slightly less reliable than the Winds of Chaos, and hie implanted some in his head.
Demise from the Wild Cards series has the power to inflict the experience of his own death (he got better) on anyone by making eye contact with them, killing them.
The Girl With Silver Eyes by Willo Davis Roberts gets telekineses and some sort of vision-at-a-distance from her silver eyes.
Sort of... Her eyes are just an outward manifestation of the mutation that occurred when her mother and four others took an experimental anti-nausea drug while pregnant. She still has an unusual eye color, but it isn't quite the same thing as this trope.
Boris Dragonasi, the big bad in Brian Lumley's Necroscope gains the power of the evil eye in the second half of the story. Earlier there was a legend told of the evil eye and how it can backfire on the user with gruesome results if it is used on someone who is already dead. Guess what happens to Dragonasi at the end of the book.
In A Wrinkle in Time, when Charles Wallace stares into the eyes of The Man With Red Eyes, he goes under the telepathic mind control of IT.
Just to make things creepier, Charles Wallace's own eyes change so that his pupils are swallowed up by the iris, giving him disturbing all-iris eyes.
The title Anti-Hero of William Beckford's Gothic novel Vathek is described as "pleasing and majestic; but when he was angry one of his eyes became so terrible that no person could bear to behold it, and the wretch upon whom it was fixed instantly fell backward, and sometimes expired." The History was first published in 1782.
Jagang, the main antagonist of most of the Sword of Truth series, has eyes which have been describes as "twin windows into nightmare". It is not surprising that his powers are essentially mind reading and possession.
In Poul Anderson's Operation Chaos, the narrator hears of a technique used on infection: they culture some of the bacteria, and then get a man with the Evil Eye to look at them through a microscope. Later, he mentions the wonders a corporation has produced, including contact lenses that allow people with the Evil Eye to live normal lives.
Michael Moorcock's Eternal Champion series includes Corum Jhaelen Irsei, who for the first portion of his career wields the eye and hand of a god in place of his own. By lifting the eyepatch he wears over this eye, he can see into a spectral place, where a creature dwells. He can then draw it out, where it will fight for him. Then the next time he lifts the eyepatch, whatever was killed by the creature has taken its place, and now IT can be summoned to fight, apparantly at a greater power level than it possessed before.
The Sibyl, in the Doctor Who New Adventures novel Time's Crucible, steals the eye from a decapitated sphinx and substitutes it for one of her own, in order to regain her waning prophetic powers.
Euron Crow's Eye of A Song of Ice and Fire is strongly hinted to have one. What's under his Eyepatch of Power hasn't been revealed yet, but judging by the reactions of his fellow Ironborn (and these are Rated M for Manly Viking expies), the fact that his regular eye is known as his "smiling eye", he's been known to consort with warlocks, and that he flies a personal standard that shows a red eye, it's a fair bet.
In Farscape Nooranti had a third eye that changed color and intermittently opened when she used her powers.
In The Lost Room miniseries, the Glass Eye is a powerful artifact that can restore/heal or destroy all flesh. Karl Kreutzfeld had to take his own eye out to use it, as the Glass Eye must be inside the eye socket of the wearer to function.
Irish Mythology: As told in The Battle Of Magh Tuireadh, Balor "of the Evil Eye" absorbed the poison of his father's druids as they were casting spells. This gave him an eye of death, which killed whoever he looked at. His eye was harnessed to bow strings so that he could open his eye properly and used it as a weapon.
The evil eye goes far back in the mythology of several countries in the Middle East, though that evil eye has more in common with a Death Glare that simply brings whoever it is given to bad luck and misfortune. Evil eye charms which ward off the effects of the evil eye are still popular in Armenia, Israel, Turkey, and a host of other countries.
Speaking of which, there are legends of an Armenian king who was able to break boulders with his evil eye.
In Ancient Rome either a bulla or a fascinum would be worn as a Protective Charm to ward off the malevolent evil that could arise from the jealousy of men, sometimes literally called Evil Eye.
Shiva, the Lord of Destruction, was forever blasting things out of existence with his third eye. Usually it was Eye Beams.
This trope is goes back to at least the New Kingdom of Ancient Egypt, when the Eldritch Abomination serpent Apopi/Apep (Apophis) was believed to have a destructive or harmful gaze. People wore and recited charms and spells to protect themselves from him. The Pharaoh also performed a ritual in which he whacked at a ball that symbolized Apopi's eyeball.
Li'l Abner featured the character "Evil Eye Fleegle", a zoot-suited New Yorker whose eyes could zap people with destructive whammies of varying degrees of power. He turned up in the movie adaptation of the strip as well.
The Eye of Vecna, from the Dungeons & DragonsGreyhawk setting, is a powerful Artifact of Doom that requires the would-be user to remove his own eye and insert it into the socket.
D&D also has the beholder monsters, which possess many eyes with various powers (including at-will telekinesis to make up for their lack of limbs). Certain variants had a class for cultists of various monstrous races that started to take on characteristics of the races they worshiped, and the beholder-worshipers grew eye stalks of their own.
4e D&D has Cyclopes and Fomorians that both use their Evil Eyes for various purposes, such as paralysis, mind domination, eye beams, etc.
In Vampire The Masquerade the vampire clan Salubri derived healing, fighting, and perception based supernatural powers from their third eye. Naturally it made them stick out like sore thumbs, and being the least evil group of vampires they were almost all wiped out because it couldn't be easily hidden. One of the survivors decided "Enough is enough!" and joined up with the Sabbat. His branch of the bloodline follows a different set of powers than the others, and their third eye looks angrier as a result. And since they aren't nearly as nice as the rest, they aren't so easily killed, so they don't care about hiding it.
The Warhammer 40000 universe has Navigators: mutants with a Third Eye, called the Warp Eye in the middle of their forehead. Apart from letting them steer ships through the Warp, these eyes kill anyone who looks into them. As a result, they have to wear a bandana when not navigating.
In addition, most Eldar tabletop psychic powers require line of sight. Mind War comes to mind; it's essentially a Farseer staring down an opponent with such intensity that it can literally wound and even kill them. On the tabletop this is translated as the opponent taking unsaveable wounds.
Zasalamel in Soul Calibur 3 has one gold eye, which contains his soul.
Some Pokémon attacks, such as Mean Look and Miracle Eye, qualify.
Generation V introduces a move actually called Evil Eye (which was translated as Hex in the English version).
The main character in Planescape Torment, being a regenerating immortal, can equip magical eyes in place of one of his original eyes. There is also a bar, at which the barkeep is holding for you an eye removed by one of your past incarnations that you don't remember-replacing one of your eyes with that one gives you an experience bonus and lets you remember part of his life.
Reisen Udongein Inaba of the Touhou series is a moon rabbit whose eyes can cause lunacy.
Jade in Tales Of The Abyss has fonic sight, which allows him to use upper-level spells with ease. He got it by applying an extremely dangerous forbidden spell on his eyes back when he was still a kid, if the picture of his bespectacled childhood self is an accurate indication.
In Meteos, the planet Meteo is basically a giant yellow space eye. Now, guess where all the planet-destroying meteors that you fend off in the game are coming from.
Jubei Akane Yagyu and her uncle Munonori of the Onimusha series both have the Oni-eyes, complete with the Eye Patch Of Power. When activated, allows extremely hightened reflexes (to the extent that time feels slowed down), illusion control (the ability to both use and see through illusions) and lethal counter-techinques (especially useful with heightened reflexes).
In Deus Ex it is strongly implied, if not outright stated that the otherwise relatively normal looking JC Denton wears sunglasses becsuse he has Evil Eyes.
In the character creation scene, you can see he has blue glowing eyes.
GoldenEye from the James Bond game Goldeneye Rogue Agent has a cybernetic eye upgraded with powers over the course of the game, with powers like seeing through walls and hacking electronics.
In the first Jedi Knight game, dark Jedi can learn a force power called Force Deadly Sight. With it activated, anyone the player sees in his vision takes damage and dies.
Alma in F.E.A.R. seems to be able to do this at will (that is kill them by bleeding them to death and blowing up everything all around her). It isn't necessarily an eye related ability, but it may as well be.
In Final Fantasy X, Seymour's aeon, Anima, has an attack where she gives an enemy an instantly fatal dose of this trope.
In Dark Souls, there are special "Eye Orbs" used to invade other players and engage in PvP. The Red Eye Orb allows players to invade and kill others, while the Eyes of Death let players curse others' worlds and generate stronger versions of typical enemies. The Ring of the Evil Eye is also said to contain a demon of the name. It lets you heal by killing people.
In Heroes of Might and Magic V and VI, the Cyclops units can be upgraded with Evil Eyes that grant them ranged attacks. Worse, unlike most ranged units, upgraded Cyclops don't suffer a melee penalty — on the contrary, they deal even more damage in melee. In the fifth game, their Evil Eyes also reduce their targets' luck.
Mary's golden eye in Shikkoku No Sharnoth gives her the ability to detect lies and see the truth, no matter how it is being hidden. It also gives her amazing intuition.
As demonstrated in the page quote, Tohno Shiki has these in Tsukihime. They have the ability to kill anything or cut along special lines. Ciel has eyes that can make you accept whatever she's saying unless you know it isn't true. Arcueid and Satsuki have hypnotic eyes. Sidestories introduce more eyes, such as ones that see the past or future.
In Dra Koi a dragon's eyes are called enchanting and the protagonist slowly seems to fall under the dragon's control. Not really. He's just falling in love with her.
While not a evil eye, per se, Miranda Deegan from Dominic Deegan has a glare that has been referred to as an "evil eye". It basically makes someone's willpower erode and derails trains of thought. Given what others in the comic have experienced, she is capable of giving someone the eye from nearly half a mile away, as well as around corners, and even from another dimension. Latest example is giving the evil eye to the The King from an unknown distance. ''
Dominic himself may have an example of this, shown early on, when Gregory first refers to their brother, Jacob.
In The Gamers Alliance, the mage Dante's eye can control a person and put a geas on his victim which forces the victim to subconsciously obey his orders. Leon learned this the hard way when he found out that all his actions during the Yamatian Invasion arc had in fact been Dante's all along.
The superpowered character Sahar (literally 'Evil Eye' in Arabic) in the Whateley Universe. Her main psychic power is the ability to make a person believe that he has been cursed. Her secondary psychic power is WAY scarier. Her eyes have red rings: the folklore sign of one with the Evil Eye. Her original reputation was that of a hated and feared villain on the Whateley Academy campus, but she appears to be trying hard to become a good guy.
Duke Phillips, Jay Sherman's boss in The Critic has an evil eye that hypnotizes people into his willing servants. It's only seen once, and played for laughs (Duke was launching a Presidential campaign at the time, and used it to get out of one reporter's question.) He even uses the trope name:
Duke: Gaze into the hypnotic power of my Evil Eye!
Professor Screweyes from We're Back. True, its actually a screw buried deep on his eye socket, but it pretty much acts as a magical eye, as he seems to be able to make magic with it (not to mention that the screw's slit is in a vertical position, giving it a Hellish Pupils look). In a deleted scene where he learn he lost his left eye thanks to a crow that pecked it out, he claims he can "watch" his biggest fear, the crows, with a "real eye and a steel eye", implying that his screw eye is far from being just a scary decoration.
Matrix has an Evil Eye in ReBoot. It provides a visual interface with is gun, including a first person perspective of the rounds moving towards the targets. Also lets him see through web shields and has tracking capabilities.