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- FLCL. Haruko Haruhara has yellow eyes. She slyly manipulates people and hides her true identity, goals and personality throughout the series.
- Ryuk from Death Note has yellow eyes and technically causes everything in the series because it's fun.
- Medusa of Soul Eater has these, which besides underlining her snake theme also reference her Manipulative Bastard nature, not to mention the horrendous treatment of her son/daughter, Crona.
- To some extent, Hikaru and Kaoru from Ouran High School Host Club (Irises) However, they're more cheeky than anything.
- Kagerou Daze: Kuroha's◊ eyes are a bright yellow. He also happens to be completely and utterly insane (and possessed by one of Azami's snakes, for bonus points). Contrast Konoha,◊ the Sleepy Head Gentle Giant with light pink eyes.
- Shuuya Kano also fits this category very well with his cat-like yellow eyes and sly, sometimes even vindictive tendencies.
- Rurouni Kenshin has Saitou, who has naturally (but not supernatural) gold eyes, tying into his history with The Shinsengumi, known as the "Wolves of Mibu". He's also quite the Manipulative Bastard.
- "Un-Go" has the character Inga who has yellow sclera. This probably has something to do with the fact he's a demon. Inga is also of Ambiguous Gender because they switch between male and female forms. Inga also seems to be a Psychopathic Man Child.
Film - Animated
- Disney uses this a lot.
- Cinderella: Lady Tremaine has yellow scleras in the scene where she takes the key to Cinderella's bedroom and closes the door before locking it. And her minion Lucifer the mean, sneaky cat has yellow sclerae by default.
- The Great Mouse Detective: The main villain of the movie, Professor Ratigan, has a yellow sclera, and has an Evil Plan to take over a kingdom.
- Hercules: Pain and Panic, the minions of the main villain Hades, have yellow sclerae.
- The Little Mermaid: Flotsam and Jetsam, the eel minions of the main villain Ursula, have yellow sclerae.
- Wreck-It Ralph: Turbo has yellow sclerae and he coined the term "going Turbo" when he tried to take over other games out of jealousy.
- Fantastic Mr. Fox: In the original book by Roald Dahl, the eyes of Mr. Fox are just black spots on white sclera but in the animated version he actually has irises. The color of Mrs. Fox's eyes is blue, while Mr. Fox has yellow eyes that emphasize his sneaky nature. With a little Fridge Logic involved, this can even turn into a spoiler: Ash Fox struggles to get his father to notice him, while his cousin Kristofferson gets constant praise from Mr. Fox. In the end, Ash manages to save the day rather impressively... and his eyes are the same greenish yellow his father has, whereas Kristofferson has light blue eyes!
- Rise of the Guardians: Pitch, the Boogeyman, has yellow eyes that glow a bit in the darkness of his lair.
Film - Live-Action
- In Good Omens, the demon Crowley habitually takes the form of a louche and cool young man in his mid-20s, but has to wear sunglasses to conceal his eyes - which are reptilian rather than human, yellow-gold with a vertical slitted pupil. He is a demon, the embodiment of all things wily, crafty and untrustworthy, and is implied to be the serpent in the Garden of Eden.
- The Berenstain Bears has an odd Double-Subversion. In ...and the Green-Eyed Monster, the eponymous monster representing Sister Bear's envy has yellow eyes.
- Amusing example in The Children Of Man, where yellow eyes are the mark of one who can use yellow magic, the magic of art, illusion, and manipulation.
- Author Simon R. Green uses this trope a lot in his fantasy series, having a particular fondness for ascribing "eyes as yellow as urine" to beings that are undead, demonic, unspeakably-vile, or all three at once.
- Foxface from The Hunger Games. Her mutt-version is noted to have amber eyes.
- Lord Foul in The Chronicles of Thomas Covenant has glowing yellow eyes that are described as resembling fangs and are his only consistently visible feature. Though Foul never directly lies, he's very good at deceiving and manipulating people regardless; indeed, his motivation for not lying has nothing to do with any sort of respect for the truth and is more about asserting his own intellectual superiority over his enemies, proving that he doesn't need to lie in order to trick them.
- The Space Wolves of Warhammer 40,000 acquire wolf-like traits from their chapter's gene-seed, such as lengthened canines and yellow eyes. Most people would have trouble believing a mob of Boisterous Bruiser, werewolf Space Vikings could be subtle in any way... and the Space Wolves are in no hurry to correct them. They're Blood Knights who would prefer an honorable battle, but they also know how to fight dirty, and when to play up their "barbarian" reputation to get people to underestimate them. There's a reason their leader Logan Grimnar ends up in charge of most wars he's involved in, even when he's not officially in command.
- GLaDOS from the Portal-series has one bright yellow "eye" on the front of her chassis. She's murdered every scientist in Aperture and forces the surviving humans to preform tests for her. She's also a compulsive liar and a Deadpan Snarker of the finest variety.
- In BlazBlue, Hazama/Yuuki Terumi sports these when he actually opens up his eyes. This is one of the signs in Continuum Shift that foreshadow his villainy.
- In Touhou Project, resident liar and (spell)thief Marisa Kirisame has yellow eyes, as does the very "youkai-like youkai" Yukari Yakumo (when they're not purple).
- Criminal Case has yellow irises on many suspects in the Oceania region, including Baxter Fraser and Veronica Salter. They are all assassins who underwent genetic treatment. Subverted in Baxter's case, as he wants nothing to do with that life.
- In the intro to Mario Power Tennis Wario and Waluigi's eyes turn yellow during moments of ill intent, something not seen anywhere else in the series.
- The Gerudo in The Legend of Zelda: Ocarina of Time are a tribe of Desert Bandits with yellow and amber eyes who also have a habit of kidnapping innocent Hylians, while their king, Ganondorf, is a Sorcerous Overlord who wants to Take Over the World. Subverted by the time of The Legend of Zelda: Breath of the Wild, however, where they keep the eye color but have dropped the thievery.
- In RuneScape, the Mahjarrat all have black sclerae and red irises... except Sliske, who has yellow irises for no apparent reason but this trope. "How do you know you can trust me? That's simple. You can't."
- The entire troll race of Homestuck have yellow sclera. As a whole they are significantly more blood-thirsty than humans, and deceit and murder are a huge part of their lives. However, the unsavory aspects of their culture turn out to be the result of an Eldritch Abomination socially engineering it to be horrible - before that, they were peaceful, making it a subversion.
- Partially subverted in Girl Genius with Dimo. He's a Jaeger, who don't have the best reputation due to their Undying Loyalty to the Heterodynes, and is a bloodthirsty killer when he needs to be. But he is loyal to Agatha, since she's a Heterodyne, which makes him a protagonist. And although none of the Jaegers are particularly intelligent, he's one of the more cunning of the ones we've met.
- Tiger from Consolers has yellow eyes, and is a sneaky Jerk Ass.
- Ratty from Mr. Bogus, which is appropriate, befitting his conniving nature.
- Socrates from Adventures from the Book of Virtues has these, to show that while he may be seem rather sneaky, he is actually shown to have a good heart because of his hidden innocence.
- Plankton from Spongebob Squarepants, despite having only one eye, would actually also count for this, as he is often scheming to steal the Krabby Patty secret formula.
- Squidward on his... sneakier days.
- Wile E Coyote from Chuck Jones' Looney Tunes has yellow eyes compared to the Road Runner's ivory white eyes, since he is always coming up with sneaky schemes to catch the Road Runner, although without any success.
- Tom Cat from MGM's Tom and Jerry has yellow eyes in his early cartoons compared to those of Jerry Mouse, often scheming against the mouse. The yellowness would disappear by the time of the Cinemascope cartoons.
- The foxes in The Foxbusters have yellow eyes, to denote that they are always scheming to catch the chickens on the farm.
- Super Mario Bros.: In all three DiC cartoons, sneaky Card-Carrying Villain King Koopa has these. He is constantly drawing up schemes, some with his Koopa Kids in the latter two series.
- Discord, the mischievous spirit of chaos and disharmony from My Little Pony: Friendship Is Magic, sports these with googly red pupils to go with them.
- Many of the villains and jerks in 101 Dalmatians: The Series had yellow eyes, including Swamp Rat and one of his henchmen, Cydne (who also happens to be a snake), Cruella De Vil (which is odd, since in the original movie she had white eyes), as well as most of her family of De Vils. Mooch also had yellow eyes to show off how much a Jerk Jock he is. Interestingly, Spot the chicken has large yellow eyes, despite being part of the main cast, as well as Sergeant Tibs the cat (yellow scleras with green pupils) who is the Colonel's most loyal rank member.
- When Dipper has his body stolen by Bill Cipher in Gravity Falls, "Bipper" gains yellow sclerae and slit pupils. It's an unusual example- Bill in his usual form has a slit pupil, but his sclera is white.
- Katz from Courage the Cowardly Dog has a pair of yellow eyes that help enhance his Obviously Evil appearance.
- As does one-shot villain Fusilli.
- Many animals have yellow eyes, and unsurprisingly, many of these animals are the types that people stereotype as malevolent. Snakes, cats and certain dogs have this quality. Birds of prey very often have yellow eyes as well, but they subvert it as they're rarely portrayed as evil.