Kanade from Asura Cryin normally has blue eyes, but when she uses her powers, one of them turns to green.
Nei in Avenger has heterochromia to indicate that she (or he, it ain't exactly clear, either) is both a Robot Girl and a real human. Well, actually, she/he is neither but has the potential to become one of the two.
Sven from Black Cat has one eye (his left) that's orange and one eye (his right) that's green. It's rather surprising that the green eye (which is a normal color for a human to have) is the special foreseeing eye, whereas the unusual orange colored eye doesn't have any powers.
His mismatched eyes are also justified in a flashback — he lost an eye in a fight years ago, the green one is a transplant.
In Black Lagoon, Balalaika is occasionally shown with her right eye glowing yellow-ish.
Invoked in Boku Wa Tomodachi Ga Sukunai, Kobato Hasegawa appears to have a red and a blue eye. However, the red eye is actually just a colored lens which she uses to cosplay as "Reisys V. Felicity Sumeragi", a vampire in her favorite show. She is seen occasionally without it on, revealing blue eyes in both of her eyes.
Nenene and Toki from Code Breaker both have one blue and one brown eye. This almost gets Nenene killed when fire bender controller Oogami mistakes her for his despised teammate Toki who is Nenene's long-lost brother. Nenene does not seem to notice the resemblance, even when Toki is standing in front of her while Sakura says "This is your brother!"
Jeremiah Gottwald in Code Geass ends up as this after he is made into a cyborg, with one orange eye and the replacement one being green. Arguably, Geass users as well, as when the Power Incontinence hits, it's usually only in one eye at first, meaning one eye will be its normal color, and the other will have the Geass symbol permanently imprinted on the iris.
Almost-example: Spike's eyes on Cowboy Bebop are slightly different shades of brown. It's very hard, but possible, to notice this before he brings it up to Faye. The reason is that one is a cybernetic replacement for an eye he lost in a very symbolic and personal tragedy.
Spike's Mismatched Eyes serve something of a plot function as well. Besides reminding us what he's gone through prior to his bounty hunting career, that cybernetic eye might explain why he's such an excellent shot with a handgun, at least when he's standing still.
This feature was brought up rather explicitly in the climax of episode 20, "Pierrot le Fou", where it is revealed that the cat that was present during the title character's horrific experiments (and was responsible for his ailurophobia), had heterochromia, leading to him freezing up at a crucial moment during the final showdown with Spike due to the light making his cyber-eye glow in a similar fashion to the cat's, allowing Spike to defeat him.
Kirie in Ai No Kusabi has very rare heterochromia which unbeknownst to him, made him a target.
Allen Walker from D Gray Man has one gray eye and one red cursed eye. Note that his eye is only red when an Akuma is around, otherwise it is the same gray as the other.
The Count from Gankutsuou. This symbolizes not only his moral ambiguity and inner conflicts, but also the fact that he is part-human, part-monster, part-alive, part-undead and part-earthling, part-alien through his symbiosis with Gankutsuou. The duality symbolism is also present in some representations of his crest, a stylized heart divided into two clear compartments with different colours to represent his remaining human feelings and the fact that he is gradually turning into a cold-hearted monster.
Albireo from Dot Hack AI Buster has one blue eye and one gold, which has to do with his name — a binary star, one of which is blue, the other gold. Kamui has the same eye color, in dedication to him. Both characters' eye colors in the real world however are unknown.
Kamichama Karin has Michiru, a brunette with one purple eye (his natural color) and one blue eye (which was implanted by Professor Kujyou after his eye was crushed beyond repair in a car accident when he was a kid).
In Katekyo Hitman Reborn! Rokudo Mukuro has a red right eye with kanji in it and a normal, blue left eye. His right eye changes the kanji to suit the number of which path's (six paths of hell) powers he is using at that moment.
The Kindaichi Case Files: Heterochromia becomes an important clue in one of the extremely difficult mysteries the titular detective is forced to unravel.
Ciel Phantomhive from Black Butler has a normal blue eye and a purple eye that holds the mark of his contract with Sebastian.
Alois later gets these when he makes a contract with Hannah, Claude, and Sebastian.
Oskar von Reuentahl from Legend of Galactic Heroes has one blue and one brown eye, which is the bane of his life — it reminded his mother of her illicit affair and drove her to suicide, which caused his father to hate him with a passion.
Rosario from Lupin III: The Columbus Files has different colored eyes for plot-relevant reasons. her left eye was discolored by the laboratory explosion that killed her mother and the peculiar red-brown color allows her estranged Mad Scientist father to identify her as his child.
In Magical Girl Lyrical Nanoha ViVid (which as the name implies, stars Vivio as the main character), Einhart Stratos also has heterochromia. Like Vivio, she has an adult form, based on her ancestry to another Belkan Ruler, Hegemon Ingvalt.
Asuna from Mahou Sensei Negima! has heterochromia. The exact significance is unknown, but it's especially notable for its absence in adaptations that don't get into her Back Story.
Volume 26's cover has revealed that Arika Entheofushia — Asuna's relative and Negi's mother — has/had this as well.
If we're counting implants, then it would be appropriate to mention Kakashi Hatake's singular Sharingan eye, which he keeps hidden under his askew headband. Ditto for Danzo. One of the other Kage's bodyguards has a Buyakugan in same setup.
As of chapter 514, Tobi has been confirmed to have implanted a Rinnegan in his left eye, while his right remains a Sharingan.
The eponymous Hellhound of Nora; when in human guise, his right eye is red and his left is yellow.
The Count D from Pet Shop of Horrors has heterochromia, one eye being purple and the other, whom he hides under his hair, is golden. In the manga, it's explained that this is meant to be representative not only for his non-human nature, but also for his inheritance: his father and grandfather have golden and purple eyes, respectively. Since each one has a very different personality, and D has personality traits from both, his heterochromia symbolizes this dual nature.
In Rosario + Vampire, the trope is played with for the villainous Kiria, who, not only have a green and a red eye, but also sports eyes with rectangular pupils, completely perpendicular to the other.
Another example seems to be Tsukune, as seen here, after being put through a body modification by Tohofuhai.
In SHUFFLE, Mayumi Thyme's mismatched eyes add to her general sense of being an oddball. The difference is more pronounced in the visual novels than in the anime.
The clone Rezo the Red Priest, Big Bad of Season 1 of Slayers has one blue eye and one yellow. Since he is blind, he has his eyes closed throughout most of the season. His magic clone thingy gets mismatched eyes after bonding with a vaguely defined 'demon-beast' that doesn't seem to actually fit into the hierarchy of evil in the world's mythology.
Copy Rezo was shown with mismatched eyes from the start, although when he first shows up, he's keeping them closed on purpose, even though he can see, because he's posing as the original Rezo. In the original light novels that the anime was based on, Copy Rezo kept his eyes closed for a different reason altogether.
In Sukisho, whenever Yoru takes over Sora's body, one of his eyes turns gold while the other remains blue.
In the second novel of Suzumiya Haruhi, Haruhi gives Mikuru one colored contact to wear during their filmed home movie, because "different colored eyes give an air of mystery". Hey, if anyone knows her tropes, it's Haruhi.
Though anyone watching the first broadcast episode alone won't know why it was there for one shot only. Other than continuity issuesHaruhi did it, it's a case of All There In TheManualLight Novelslight novels or second season. In the context of the film, Mikuru had the ability to shoot laser beams from that eye. Then Haruhi's Reality Warper powers kick in and actually bestow this power on the contact lens. That sudden flash of black after Mikuru fires the "Mikuru Beam" is Yuki catching the laser with her hand before it can impale the cameraman (Kyon). She then tackles Mikuru to remove the lens and inject her with nanomachines so that it doesn't happen again (note: it does. At least three times). The film is full of examples of Haruhi unknowingly using her Reality Warper powers to bend the world to her script (like how she managed to get a perfect cherry blossom shower for her final scene despite it being wildly out of season) and is the reason why Kyon makes her read that "this is a work of fiction" disclaimer at the end... twice.
Syaoran of Tsubasa Reservoir Chronicle has differently shaded eyes to signify how one is blind. This further symbolizes how he only has half a soul, donated to him by the real Syaoran, of whom he is a clone. When the real Syaoran awakens, the Syaoran we've been seeing not only turns evil, but rips out Fai's eye (containing his magic) and eats it, turning his blind eye blue.
By the last chapter of the manga, it's possible (although not confirmed by a color image) that Fai has this too, with one golden and one blue eye: he gave up the magic -thus the blue color- contained in his remaining eye, turning it permanently gold, then got his blue eye back from the Syaoran clone. However, it seems implied that the gold color came from his vampire blood, which Yuuko said might be overridden once he got his magic back, so maybe this would make both his eyes blue again, or possibly one blue and one a neutral color, but since he gave up the other half... yeah, TRC is complicated.
Big Bad (of at least one arc) Rido Kuran of Vampire Knight has one blue eye and one crimson eye, a trait that shows up in the people he possesses. This is the first clue to Rima Touya that something's not quite right about Shiki...
Lord Darcia of Wolf's Rain has one blue eye and one golden wolf's eye, to show that he's found a way to turn himself into a wolf so that he can enter the Paradise forbidden to humans. Fortunately his plan is thwarted by Kiba and Cheza, but his evil wolf eye lives on...
Watanuki in Xxx HO Li C loses his eyesight in one eye and eventually comes to share half of Doumeki's right eye to "fix" this, changing one of his eye colors. This is shown in the black and white manga by one of his pupils being incompletely inked. If you think this is coincidence that it resembles Tsubasa Reservoir Chronicle, Yuuko would like a word with you.
CLAMP loves this trope. In X1999, Subaru has one green eye and one brown eye that once belonged to Seishirou.
These characters are from Tokyo Babylon and there is a detailed reason as for why there are like this. Still count.
In Yami No Matsuei, gate keepers can be identified by their different colored eyes. Wakaba has an orange right eye and a brown left eye.
The Yu-Gi-Oh! villain Dartz has one golden eye (his natural eye color) and one that was turned pale blue by the whole Orichalcos incident. And, if false eyes count, let's not forget Maximillion Pegasus, who has one brown eye and one Millennium Eye.
Yu-Gi-Oh! GX: Yubel has one orange eye and one green eye. In Season 4, after Judai merges with Yubel, his normally brown eyes change to these when using his newly acquired Green Lantern Ring powers.
Yu Gi Oh Zexal uses these as a recurring visual motif. Most people get the effect from the Augmented Reality eyepieces they wear while dueling, but Astral has them naturally (one eye's gold, the other glows white along with that entire side of his body) and most major antagonists seem to have their actual eyes change color instead of wearing an eyepiece.
In the manga Enchanter by Izumi Kawachi, if you become an enchanter, one of your eyes changes, turning deep red with a pinpoint pupil. Oddly, long-time friends don't seem to notice the change.
Yakumo in Psychic Detective Yakumo has one normal brown eye and one red eye which he usually conceals with a colored contact lens. The red eye can see the spirits of the dead.
In the Distant Finale of Gurren Lagann, Simon has developed one spiral-shaped eye similar to Lord Genome's, likely to convey that he has mastered Spiral Energy.
In Rental Magica, Itsuki was in an incident that turned his right eye into something demonic looking. Before that, said eye was still an unnatural red.
In Another, there's the reverse-boatlights variant, when we find out that under Misaki's Eyepatch of Power, hides a green clairvoyant glass eye (from a doll), in contrast to her right normal red.
Masato Kadowaki from Arata Kangatari gets these later on in the story after one of his original eyes is torn out.
Deliberately invoked by Rikka in Chuunibyou Demo Koi Ga Shitai. She has a perfectly normal pair of blue eyes, but frequently uses yellow contacts on her right eye (which she in turn covers with a medical eyepatch) as part of her "Evil Eye" gimmick.
A lot of characters in Kiddy Girl-and have oddly colored eyes, but they get outmatched by Letuchaia and Pauki, who have eyes with a very clear horizontal split in them and the lower halves have differently-colored internal half-rings (sectoral heterochromia x2). Geacht'er has a slightly less conspicuous version of this, for some reason.
Edehi Bootsvorz from Future GPX Cyber Formula has a normal eye on his right and a cybernetic eye on his left that replaced the eye that was lost in a test drive accident. In SAGA, he gets a more-natural looking transplant, giving him a blue and gold eye.
Neko from K has a green right eye and blue left eye in her human form, which makes her look far from normal. She's not, of course, and is quickly identified as a Strain, an individual with supernatural powers that were not given by a King. Her specialty is creating illusions and modifying the memories of the people around her with her presence.
Ren Hakuryuu in Magi - Labyrinth of Magic has a realistic variation in which one of his blue eyes is much lighter than the other due to trauma.
Vincent Nightray in Pandora Hearts was abandoned by his parents due to one of his eyes being red, a sign of him being a child of misfortune. His other eye is yellow.
Gisen's patched eye is red. She can also use some powerful spells with it.
In the final episode of the first season Jubei gets one eye coloured for each of her two personalities, signifying that both are in power. Asskicking ensues.
Delirium of The Endless, from The Sandman. It's part of her overall chaotic look. This disappears when she pulls herself together to be serious. She hates doing this as it is hinted it actually causes her physical pain. Both lampshaded and subverted, as one line specifically states she can't remember which eye is supposed to be green, which one is blue and where the silver sparkles go. If you watch carefully, they do reverse from time to time. At one point, after realizing she can't remember which eye the flecks are in, they aren't in her eyes for the rest of the story.
Nicodemus West in Doctor Strange: The Oath has one brown eye and one blue.
Films — Animation
A nonhuman/humanlike appearance example: in Shane Acker's Nine, the rims of 6's lense eyes are mismatched in color (one is more gold-ish, while the other is a gray color.) They're also different sizes.
Films — Live-Action
In 28 Weeks Later, the mother and her son have heterochromia. When she becomes a vector for The Virus, it serves as a clue to her and her son's shared biological resistance to the virus, and an indicator of when they become exposed but remain unturned: one eye becomes bloodshot like a normal zombie'sinfected would, the other remains clear.
X2: X-Men United: Jason Stryker has differently-colored eyes, as does the illusory little girl he creates.
In X-Men: First Class Charles Xavier flirts with a (normal human) co-ed with one bright green eye and one blue eye. His jealous shape-shifting pal Raven AKA Mystique alters one of her "brown" eyes to golden yellow.
Supernova: A device meant to protect a single user from the stresses of light-speed travel is used by the two main characters despite warnings that such misuse can result in a merged Body Horror. (The others were busted.) Of course, that'd have been a majorDowner Ending, so only some minor merging takes place, resulting in their exchanging an eye, each now having one blue and one brown.
In Wayne's World 2, Wayne and Garth need to organise their concert with a guy who has partial ocular albinism (one eye has no pigmentation, i.e. is white). Hilarity Ensues when they get distracted by this while pretending they barely notice and make several Freudian slips.
Wayne: Well, we'll go through these forms with a fine toothed comb, cross the "t"s and dot the... lower case "j"s.
In The Unborn, the 2009 film, this trope is one of the indications that the protagonist is being haunted by the title unborn twin brother who is trying to possess her.
In Vicky Cristina Barcelona, Maria Elena (Penelope Cruz) tells her ex-husband that she doesn't trust his new girlfriend Christina because her eyes are of different colors. Then again, she's a tad crazy.
Brad Dourif's Wormtongue in The Lord of the Rings was meant to wear two pale blue contacts until the costumers discovered he looked creepier while wearing only one.
In Practical Magic, young Sally Owens cast a love spell for a man she thinks can't exist, by giving him very uncommon traits. One of these is that he'd have "one green eye, and one blue". Twenty years later, guess what color eyes Detective Hallet has?
The film Redwood Curtain, based on the play by Lanford Wilson. (See "theater" section below.)
In District 9 the iris of Wikus's left eye turns gold (and huge) at around the seventy-second hour of his transformation into a Prawn. This trait is one of the ways the audience can identify him at the end of the movie.
In Don't Look Back, the characters' appearances slowly change over the course of the movie. Characters who are midway through their transformations often have mismatched eyes.
Lucie has them in Livid. Her heterochromia is described by another character as a sign of her having two souls.
The protagonist of Shutter Island describes Andrew Laeddis, the madman who killed his wife, as having mismatched eyes. Subverted in that the description is a fabrication dreamed up by the protagonist, who is Laeddis but is in complete denial of that fact.
The hitman in Mulholland Drive is having one blue and one brown eye in the first part of the movie. In the second part his pair of eyes are blue.
Achmed 'the Snake' from Elizabeth Haydons' Symphony of Ages has mismatched eyes because he is a crossbreed of 2 very different species. The color isn't given, but they are described as being different shapes. Being a freak wherever he goes forms a big part of Achmed's character.
Chip, the hero of Ira Levin's novel This Perfect Day, has one brown and one green eye. This causes him some embarrassment, since he lives in a world where genetic engineering and restrictions on who may reproduce have produced a world of near-identical people, all of whom have brown eyes. He eventually has the green eye replaced by a brown one, as part of a scheme to lull the Big Bad into thinking he was finally accepting his role in society.
Tyrion Lannister from A Song of Ice and Fire has one green eye and one black one. This may come from either heterochromia or partial aniridia, and are among several other congenital defects with which contribute to his nickname of "the Imp". That aside, Tyrion sometimes uses his eyes to unsettle and intimidate people when it serves his purposes.
Euron "Crow's Eye" Greyjoy hides a black eye behind an eye patch. His other one, called his smiling eye, is blue.
Minor character Shiera Seastar has one blue eye and one green eye, supposedly due, in part, to her rumoured black magic.
Nanny Ogg's cat, Greebo, also has mismatched eyes, one's a normal yellow cat's eye, and the other is pearly white and blind, presumably due to one of the many fights he's had with animals much bigger than him.
In the Star Wars Expanded Universe, Gaeriel Captison has mismatched eyes. They're constantly referred to in the book in which she's Luke's Love Interest, possibly indicating that Luke finds this an attractive feature. As does villainess Ysanne Isard, main antagonist of the X-Wing books. The right is blue, and the left is red. They're often symbolically attached to the cold efficiency (her nickname is Iceheart) and fiery anger she's known for.
Gaeriel's daughter, Malizna, inherits the eye colors. Whether this has to do with genetics, The Force, or simple coolness isn't really clear.
The cat in Jon, Flora and the Odd-eyed Cat (pink and blue).
In Black Dagger Brotherhood, Quinn has one green, one blue eye; though described pretty often as beautiful, in a world where any 'imperfection' is treated as a shame on the family, he is neglected his entire life because of them and eventually disowned- leading to his practically paralytic lack of self worth and massive tendency towards overcompensation. Eventually they seem to have a point, as he [[sppoiler: starts having visions.]]
In the third book, The Eternity Code, Artemis has one blue and one hazel eye because of an iris cam.
In the fifth novel The Lost Colony, this happens more permanently when he gets one of his eyes switched with another character as a result of interdimensional travel.
In one Flashman novel, the fairly nasty Russian villain Nicholas Pavlovich Ignatiev has one blue eye and one eye which is half-blue and half-brown. Notably, Ignatiev is an actual historical figure, but his eye colour is not recorded in history, allowing the author to take a few liberties.
As an allusion to this, the villain of The Peshawar Lancers, one Count Ignatieff, has a blue eye and a brown eye.
In the book The Wild Road one of the characters, Mousebreath, is a male Tortoiseshell cat with an orange eye and a blue eye.
In Sarah Monette's The Doctrine of Labyrinths, the wizard Felix Harrowgate has one blue eye and one gold eye. The blue(?) eye is a result of an injury, so mostly blind. The colors give him no specific powers, but it does freak people out.
The horribly inbred Martense clan from The Lurking Fear by HP Lovecraft all have this as a distinguishing mark. They have brown-and-blue eyes apparently. This is the tip-off that the swarm of Humanoid Abominations haunting the area actually consists of their offspring.
In Kristin Cashore's Graceling, all "Gracelings" have this as a distinguishing characteristic. It becomes important to the plot when you find out that one of the kings is missing an eye, and it later turns out that he is Graced with a very effective version of Charm Person, as it can work even second- and third-hand, via rumors.
The Known Space novel Juggler of Worlds by Larry Niven and Edward M. Lerner reveals for the first time that Nessus, whom Niven created 41 years previously, has one red eye and one yellow eye. (Being a Pierson's Puppeteer, he has two heads with one eye each.)
All the clone "shatterlings" of Gentian Line in "House of Suns" by Alastair Reynolds have one green eye and the other a "wintery jackdaw blue", since they're all male and female "facets" of Abigail Gentian. it is noted that since they have a bit of leeway from Abigail's exact appearance, in some shatterlings the mismatched eyes are toned down so much as to be unnoticeable
Evil Diogenes Pendergast from the Agent Pendergast novels by Doug Preston and Lincoln Child, has one hazel eye and one pale blue eye. It's revealed late in the series that pigment loss in the blue eye is due to an injury which blinded him.
One Goosebumps book has the main character's best friend be a girl with Mismatched Eyes. This becomes a plot point when she mysteriously disappears and he starts seeing a dog with Mismatched Eyes around the neighborhood.
In the Roger Zelazny book This Immortal, protagonist narrator Conrad Nomikos has Mismatched Eyes, among other odd features. But then he is probably a mutant and is definitely hundreds of years old. His unique appearance is an important plot point.
I glare at people through the cold blue one on the right side when I want to intimidate them; the brown one is for Glances Sincere and Honest.
Giulia in Mika Waltari's The Wanderer has different-coloured eyes. She's an evil bitch, though, like most female characters written by Waltari.
In Nancy Springer's I am Morgan Le Fay, Morgan has one violet eye and one emerald green one, which marks him as a fay. They're also described as very dark, so people actually have to look right into her eyes to see the difference.
In Julia Golding's Companions Quartet, several of the main characters have mismatched eyes, including Connie, the heroine (green and brown), her best friend Col (again, green and brown), and the villain Kullervo (green and gold)
In Jean Kerr's play King of Hearts:
Dunreath: My left eye is blue but the right one is brown. Didn't you really know that? Larry: You're kidding. Good God, they are different! Dunreath:(defensively) Well, it's not a disease!
In Quinn Fawcett's Mycroft Holmes novels, Paterson Erskine Guthrie, Mycroft's secretary and amanuensis, has mismatched eyes.
"Mirror twins" Eleda and Adele in The Truth-Teller's Tale by Sharon Shinn have these. Adele has a left blue eye and right green eye and Eleda has a left green eye and right blue eye.
In Jostein Gaarder's philosophical novel Maya, the character Laura has one brown eye and one green eye. The narrator thinks of this as somehow connected to her dual nature - one side of her seems to care for all living things and the planet as a whole, while the other side seems to care about everything in the world except human beings.
Hnick from Dmitri Yemets's book series Methodius Buslaev has one blue eye and one black eye according to book 3. Romasjusik is also described as having one golden eye and one orange eye. Both cases aren't natural, since the latter has artificial body, while former's body is stitched from at last two different corpses.
Ace Diamond from Double Crossing by Meg Mims has one blue eye and one green eye, the green being the result of an old injury as a child in Texas.
In the Skulduggery Pleasant (books 'dark days' and 'mortal coil') there's Davina Marr, who is discribed twice as having heterochromia, but the colours of her eyes are never specified. It's signficant to her role/character seeing as she does possess magic powers, although she is far from the only one in the series.
'Alex' in the Bill the Vampire series, has one brown eye and one green. It turns out he's Alexander the Great.
In Babylon 5's later seasons, G'Kar loses an eye to Centauri torture; when he receives the replacement, it is blue instead of red (due to supply shortages), giving him no end of consternation and a singularly unbalancing countenance. He's quite relieved when a second replacement, of the right color, arrives.
Chief Inspector Derek Conway in The Bill had this condition, mainly because the actor who played him did as well (and they didn't want to bother mucking about with contact lenses trying to make his eyes the same colour).
In one chapter of Goosebumps TV adaptation, there is a girl, best friend of the protagonist of that episode who has different coloured eyes, one blue and one in a darker greenish tone. That's because she is in fact a huskie dog, and all the kids in town, protagonist included, were puppies genetically modified to become human.
Lieutenant Aiden Ford of Stargate Atlantis has one eye turn completely black due to an accident during a Wraith attack on the city. This same accident also got him hopped up on and addicted to Wraith enzyme, causing him to go AWOL and hunt down the Wraith on his own.
The 1999 ITV miniseries adaptation of Oliver Twist gave Edward "Monks" Leeford one brown eye and one blue eye. Funnily enough he was played by Marc Warren, who went on to play Jonathan Teatime — another character with mismatched eyes — in the film adaptation of Terry Pratchett's Hogfather.
From CSI: Crime Scene Investigation, Lady Heather's daughter has one brown and one blue eye. This becomes a horrific plot point when the daughter becomes a victim of an insane Mengele wannabe who prefers his women with two blue eyes.
"Ian Moone", a recent villain on the series, has one blue and one brown eye. In this case, it's presumably done to make him recognizable to the audience, as he wears a skin-tight bodysuit and full-face mask.
Luther. Alice Morgan puts in a single colored contact lens when carrying out her Sickbed Slaying, presumably so the police officer she speaks face-to-face with will remember this unusual detail rather than her actual features.
An episode of Medical Incredible had an episode that included this. While one could not tell by looking at the boy, if you looked in photographs, he had Mismatched Eyes. His mother thought this was very strange because it kept showing up in every single photograph, and only in photographs. Everyone else thought it was just a trick of the light or a camera flaw, but she knew something was up, so she finally insisted that doctors check his eye in case there was something wrong. Turns out, this was because of a rare eye cancer. You can rest easily - because they caught it early, they could cure it, and the boy is alive.
Murdoch Mysteries, "Belly Speaker": The murder victim and his son both had one brown eye and one blue eye. The son's puppet which looked just like him had mismatched eyes as well, only blue and dark grey. They were all very creepy.
Murdoc Niccals of the virtual band Gorillaz has two different colored eyes, one black and one red.
2D temporarily had this during his coma year, as one eye was normal and the other fully black due to a fracture.
David Bowie, possibly the most famous real life example, doesn't actually have true heterochromia. His left eye has a permanently dilated pupil, the result of being in a fight, that gives him the appearance of having two different colored eyes, making one look to be darker (sometimes dark blue, sometimes brown) than the other. For a clear view, look closely at the cover of 'Black Tie White noise◊'
Marilyn Manson sometimes wears non-matching contact lenses to look as if his eyes don't match.
WWE wrestler Kane has one light-blue eye and one brown eye, with the pupils being slightly different sizes (an effect achieved by the wrestler wearing non-matching contacts, like Marilyn Manson). Early in his run, it was implied that the blue eye was actually damaged by the fire which had "scarred" him and that the eye was actually a false eye. This was ignored as the years went on, and now the mismatched eyes aren't even commented on at all, but because it's such a well known feature of the character, it has remained despite no longer even seeming to matter in the character's admittedly screwed up history.
Similar to Kane, there was Glacier from WCW, though he had a martial-arts gimmick and dressed to look like Sub-Zero. He wore a blue contact lens over one eye; when his gimmick had been run thoroughly into the ground, he "sold" the contact lens along with his mask and "armor" he wore during his entrance, to another wrestler. The fact that he gleefully hawked off the garb that had BEEN his character for over three years was just one of the first instances which showed which direction the newly arrived Vince Russo was planning to take the company.
In the world of Marus, as depicted in Adventures in Odyssey's Passages tie-in episode, different-colored eyes are recognized as a sign of prophecy. Interworldly interloper Alice physically goes from having brown eyes to blue and green, then loses them again when her time as The Unseen One's messenger is up.
Shelyn, the Goddess of love and beauty in Pathfinder sometimes appears with one blue eye and one silver eye.
Valerie Rose from the Fantasy Strike games (Flash Duel, Puzzle Strike and Yomi) has one blue eye and one green eye, and is canonly stated to have heterochromia.
The play Redwood Curtain is centered on a young Vietnamese girl who was adopted by an American family. She has "eyes like a husky dog" (one blue, one dark). When she meets a homeless Vietnam vet who has similar eyes, she starts wondering if he could be her biological father. He's not, but he knows who is.
In the Toronto production of We Will Rock You Commander Khashoggi has this, which may explain why he wears sunglasses for most of the production
In Quintessence: The Blighted Venom, Kardian (Alden) performs an operation on Lunair using Reivier's eye to cause her right eye to turn green whenever Shanti takes control, as a warning.
An updated artwork of Louis Cyphre from Shin Megami Tensei II shows that he has a red pupil on the right, and blue on the left to indicate that he's no he.
Yuna from Final Fantasy X has heterochromia to indicate that she's half Al-Bhed. She has a green eye and a blue one.
Marx from Kirby Super Star is frequently depicted in fan art as having one blue eye and one red eye, either matching or opposite the blue and red sides of his hat. However, in the official artwork and sprites, both of his eyes are purple.
Shiki from the Samurai Shodown series has naturally blue eyes, but one of them is red, indicating her mind being possessed by Yuga the Destroyer. The other stays as it is because she struggles to prevent her mind from being completely overtaken.
The vampire sisters in Castlevania: Portrait Of Ruin have heterochromia to indicate they aren't full vampires yet. Each of them has one eye of the other's normal colour, creating a creepy impression that they've switched eyes.
Lady and Arkham from Devil May Cry 3 have heterochromia. It doesn't actually mean anything... but it serves as an early clue that they're father and daughter.
It also serves as a visual hint that Arkham is Jester.
Katina Tarask in Super Robot Wars Original Generation. As of yet, no significance has been attributed to her character, but the fact that she was the winning design of a fan-submission contest may be explanation enough.
Levi Tolar, on-again off-again Dragon, originally from Super Robot Spirits, has one red and one golden eye, to match her mecha Judecca. Her eye color changes fairly regularly though, depending on game and whether her Levi personality or her Mai Kobayashi personality is dominant.
Bitores Mendez, the village chief from Resident Evil 4, sports one blue eye and one red. The red eye is a falsie, though.
In Fallout 3, Dogmeat has one blue eye and one brown. So do all dogs with his character model, for that matter, continuing on into Fallout New Vegas.
Ballos from Cave Story has one eye stark white, one eye stark red, neither with any visible pupil. It's probably less about his biology and more about making him look even more otherworldly than he already is, though.
The Demon Crown has one eye set in it, that is the same color as his remaining red eye. Fanon suggests that he set one of his eyes in his crown.
Ranulf in the 9th/10th Fire Emblem games has one Blue and one Pink/Purple colored eye. Though this is, plotwise, insignificant, a bit of reading implied that this led to potential blindness in cats, which may explain why he got his ass handed to him by every significant bad guy (and one good guy) despite being implied to be one of the strongest among Cat laguz... i.e. he keeps losing because he can't see worth a damn.
That's deafness rather than blindness that is connected with heterochromia in cats. Actually, it has to do with the genes that give cats white or white spotted coats. That genetic set up also allows for heterochromia and increased risk of deafness. Might still be a factor, though I only remember him getting really trounced by The Black Knight/Zelgius. He pretty much owns everyone else.
I always assumed it was a nice touch by the artist due to the fact that heterochromia is common in real life cats.
Also from the Fire Emblem games is Idoun one of the enemies in the 6th game, who has a red eye and a green eye. (It might actually be blue, but with sprites it's a bit difficult to tell.)
Dr. Loboto from Psychonauts wears goggles that consist of one green lens and one red lens, to highlight how abnormal he is in a world of already-freaky-looking people.
Psychonauts is full of people with mismatched eyes. Bobby Zilch as another one, as well as Coach Oleander and Linda.
Yuber in Suikoden III has one red eye and one silver one. He's also not human.
Ragna the Bloodedge of BlazBlue has these to indicate that he is half-Vampire. However, this only applies in one particular instance of the Stable Time Loop: in all others, including the one covered by the story, his changed eye, the red one, is linked to the function of his arm, the fake Azure Grimoire. When it stops working, so does his arm.
Atsuki from Lux Pain has a gold eye (his right), and a black eye (his natural color). Justified, in that in the power of Lux Pain made his right eye gold.
Mass Effect 2's DLC has Zaeed Messani, who has one brown eye and one pale grey eye. The paler eye is implied to be a cybernetic replacement installed after he survived a shot to the face.
Dr Betruger from Doom 3 has one eye that is not only a different colour, but has no pupil. Creepy, eh?
Sting Chameleon, from the Mega Man X series, has an odd version of this. Being a robot, one of his eyes looks normal, but the other looks metallic and appears to have an irising lid. The irises, however, are the same color.
He has one normal eye and one chameleon eye.
In Deadly Premonition, Zach is eventually revealed to have different-colored eyes, his left eye having been damaged in a childhood trauma.
In Ragnarok Online, the pope of Arunafeltz and her twin brother has opposite-color heterochromia. Apparently, this was one of the reasons she was chosen as pope. The other reasons was her hair and skin color.
The main character in Homura has these in order to symbolise his half-human half-angel blood.
The Masked Man of MOTHER 3 is commonly depicted with these, while they're nowhere to be seen ingame. Even when he takes off his mask. It might be because his eye glowed before he attacked you at Chupichupyoi.
Resonance Of Fate allows players to change the colors of the main characters' eyes individually, thus creating quite a few options for mismatched eyes.
Puyo Puyo has Sig, who has one red eye and one blue eye.
There's a few examples in Vampire The Masquerade Bloodlines. The Voermen sisters have blue and green, Mister Ox has grey and amber, and the Malkavian and Nosferatu PCs have blue and brown.
In Tales Of Graces, this is a sign that Lambda is inside somebody's body. It happens to Richard and later Asbel, and this carries into Tales Of Graces F. When lambda is inside Richard, his other eye is red, but when it happens to Asbel, it's actually purple, signaling that Lambda has a different relationship with Asbel than Richard.
Vanessa of Luminous Arc has one grey/purple eye and one red one, but this doesn't seem to indicate anything beyond being just as loud and noticeable as the rest of her.
Ironhead from Swim Ikachan has a right red eye and a blue left eye, although you couldn't tell the latter's colour in his cameo appearance in Cave Story, since it can only be seen when he's facing left.
Johnny Powell in The Darkness 2. They're both blue, but his left eye's abnormal.
Handsome Jack, the primary antagonist from Borderlands 2 appears to have heterochromia. His left eye is green and right eye blue.
This serves as foreshadowing that Jack's face isn't real. The blue eye is his actual eye while the green is part of the mask. His actual left eye is scarred and appears to have no pupil.
Fight or Die: Yuko Amano has a red left eye and a blue right eye. Though she has normal blue eyes in a flashback.
Do note that that her body is in Lucifero's possession and that the red eye is that of Lucifero's. Yuko's blue eye is the normal one.
Earthworm Jim sports a strange variant of this trope. His left eyeball has a green iris and black pupil while his right lacks an iris and has just a black pupil.
Maple Story's Luminous starts his story off with two blue eyes, then one of his eyes turns red when he absorbs the Black Mage's energy.
Mary's normally blue eye right turned to gold six months before the story started in Shikkoku No Sharnoth. The golden eye is somewhat magical and a macguffin throughout the story. Near the end, Charlotte's left eye also turns gold, but it changes back eventually.
In Phoenix Wright: Ace Attorney DS, Angel Starr has differently colored eyes, but it's hard to tell because the eyes are tiny and we only see one eye at a time. (When the hair covers the right side of her face, she looks nice, but when she's angry it covers the left, so we never see them both at once.) According to the creators, it's because she wears colored contacts.
Mannick from Charby The Vampirate has a red right eye, and grey (blue in some comics) left eye. It doesn't appear to mean anything in particular.
Sifris from Pink Black has a blue eye and a pink eye. This is never really noted or explained, so it is possibly normal.
Topaz from Monsterful; she has a two shades of the actual gemstone her name refers to, her left eye is light yellow and her right one is sky blue.
Ashley Freyja of Cry Havoc has one blue eye and one green, and while never actually mismatched, the werewolves eyes fluctuate between their natural color and yellow when angry or excited. Psychers eyes glow blue when they are using their powers.
Most of the Val'Sullisin'rune family in Drowtales have mismatched eyes, a fact that is commonly known in the setting and referred to as "devil eyes" in the case of the Ill'haress Ash'waren. It is not clear that they have any sort of "dual nature".
In the case of Ash's daughter Faen, the dual personality Blue = Innocent / Purple = Mysterious or Badassfits.
Kade from Eerie Cuties has a yellow/gold left eye and a blue right eye. Of course, he is a Werecat...
The chimera boy Archie from Ellen's second life dreams in El Goonish Shive, although he hasn't been drawn in colour yet, appears to have heterochromia, given that one of his eyes is filled, and the other has a pupil and a gap between the pupil and the outline of the iris.
Vladic from Emergency Exit. This could be normal for his species for all we know...we've never seen both eyes of the only other Merf character.
Skye from Far Out There has one green eye and one purple one. In her case, the difference is quite practical: the purple one has x-ray vision.
Prism from Flaky Pastry has one violet eye and one cyan eye.
The title character of Kokiro has heterochromia and wings.
Sudoku (Jigsaw's sister) in Last Res0rt also has heterochromia, with no special explanation attached other than her father (Cypher) having green eyes and her mother (Meridian) having blue. She's the only one in the family with this trait though.
Maureen from A Modest Destiny. She hides her blue eye because blue eyes are considered evil. It disappeared though when she had her baby.
Kimiko of Dresden Codak has one brown natural eye and one blue mechanical eye as of the "Dark Science" arc, though originally her natural eye color was blue and thus the synthetic one matched when it originally showed up. Aaron Diaz retconned it so the synthetic one would stand out more.
Feral from Strays. His green eye is natural,the red one was caused by something else. Feral, being mute, can't tell us what.
Berri in Fiyora Nya has one red eye and one green eye. Though they apparently change colors due to her other souls.
In a variant, Lilith/ Judy in Girl Genius has eyes that are mismatched in size, due to being a construct. She wears glasses that make them look like they're the same.
In Doomsday My Dear the main character has one blue and one green eye because this is a trait of a carrier of the Blood Plague. Several other characters turn out to have this undesirable trait as the comic progresses
Chev from Papi Nyang has one blue/green and one yellow eye.
In Pulse, while it seems completely natural, tall blonde super-heroine Tabitha "Bolt" Greene has one green eye and one blue eye.
Jolene Brooks of Between Failures reveals that she has this - while one eye is a light amber color, the other is nut brown. She wears color contacts to disguise it - sometimes just a dark brown one to cover the amber eye, but usually something more exotic, like purple. It's a major contributor to her shyness issues.
Dabbler of Grrl Power has mismatched cat-like eyes, the right one green and the left one blue. But that's not as unusual as the rest of her, given that she's a four-armed part-succubus superheroine.
All the Ravens (servants of the Raven) in Archipelago are inflicted with a left eye with a black sclera and a glowing red pupil, regardless of species. At least some of them can hide this to pass in normal society.
Chaz Villette from Shadow Unit has one brown eye and one greenish-hazel.
Achmed the Snake from the Rhapsody Chronicles has eyes that are not only mismatched in color, but also in size, shape, and quite probably, species. Also, a face that looks like scar tissue, apparently.
Hawley Faust from Survival of the Fittest has this, though outside of Epileptic Trees which might be true (most arguing that they symbolize Adam's nature pre-game and post-game) it has no actual significance.
As does Dominica Shapiro, who was much more dual in nature (displaying both a thoroughly villainous and surprisingly heroic side).
In version four, Charlene Norris has one blue and one green eye, while Clio Gabriella has one green and one hazel. Dave Morrison in the same version has a minor form.
Evolution's Child from SCP Foundation. In addition, sclera of one of her eyes is black.
Techno-Devil of the Whateley Universe has one eye that's a solid red cybernetic implant. He's only fourteen. He's a mutant too, so his other eye doesn't look normal either. In his case, it signifies that he's the son of the notorious supervillain Dr. Diabolik, and darn proud of it.
Cigarettes the Cat, a creation by John Kricfalusi. Left eye red, right eye blue.
Several characters from Homestar Runner such as Marzipan (one of her eyes is larger than the other), Bubs (one blue eye and one black eye), the Poopsmith (one black eye and one white eye), and Hyperactive Strong Sad.
Arkada's avatar for his mailbag showdowns and the like has one green eye and one blue eye. Questions asking about whether he has this in real life (it's hard to tell in his live videos) gets you a Mathematician's Answer