The Adventures of Super Mario Bros. 3 episode "True Colors" is obvious to the point of parody. Kooky von Koopa and Cheatsy Koopa fly around painting half the Toads (and Luigi) red and half (and Mario) blue. They then disguise themselves as red and blue Toads to stir up resentment between the two halves of the population. The conflict is resolved when the Mario brothers manage to get the Toads to rally in defense of their princess. The similarities to real life racism is anviliciouslylampshaded in the end by the brothers ("Think they'll ever learn that lesson in the real world?").
The premise of A Kind Of Magic is a fairy-tale family who had to move to the real world because of fantastic segregation: The mom is a fairy and the dad is an ogre, but interracial marriage is apparently outlawed in Fairyland.
In Alfred J Kwak, the titular character travels to a country called Atrique, where the original inhabitants, the black ducks, are under the oppressive and discriminative authority of the white geese. It is obviously South Africa before the abolition of Apartheid (the series was produced in the late 1980s), just with humanoid animals.
Steve: I like the Berenstein Bears as much as the next person, but I'm not gonna let one of them marry my daughter.
A subtle theme in the "Chicken Boo" segments of Animaniacs. Boo usually excels at whatever career he takes in his disguise, and is beloved by everyone who talks about him. However once he's outed as a Chicken, everyone turns on him, even to the point of siding with the oppressor that Boo had saved them from moments before.
The Fire Nation consider themselves to be superior to all of the other nations, to the point they killed off an entire race of benders (except Aang).
It goes both ways as well. Zuko saved an Earth Kingdom town and was praised until they discovered he was not only a firebender, but the Fire Nation Prince. They would rather be oppressed by Earth Kingdom soldiers than saved by a firebender.
Jet is extremely prejudiced against the Fire Nation.
Sokka experiences a bit of culture-based prejudice in "The Siege of the North". While they're of the same race, Yue's fiance clearly thinks the Southern Tribes are inferior.
In the canon interquel graphic novel series Avatar The Last Airbender The Promise, the racism gets spread around. Earth Kingdomers are second-class citizens in the Fire Nation colonies, Smellerbee calls firebenders "those ash-makers," and Sokka gets a brick thrown at him by an Earth Kingdomer who calls him a Water Tribe savage.
Tarrlok, who represents the extremist, xenophobic faction of the benders, and takes advantage of the growing current of anti-Equalist sentiment to establish his own rule over Republic City.
The villains of the first two seasons of Ben 10 Alien Force, the Highbreed, are essentially a G-rated version of the Yuuzhan Vong. They think every other species in the universe is inferior to them. Unusually, they were content to merely avoid contact with other species in the past. The reason they started their campaign to "cleanse" the universe is because they discovered that their species has become sterile and will go extinct in a generation or two. They just can't stand the idea of "inferior" beings outliving them.
The dingoes in Blinky Bill. But most of them are troublemakers with the exception of poor Shifty.
In Bravestarr, a Space Western with a Native American hero, the indigenous "Prairie People" of New Texas (gnomelike sorts that burrowed like prairie dogs and had a vast underground kingdom) were the stand-ins for Native Americans, indigenous people treated with prejudice by the settlers.
In Capitol Critters a few episodes dealt with a gang of rats at war with a gang of cockroaches the roaches were meant to symbolize minorities in general some spoke in African, Italian, Hispanic, and Yiddish accents, they constantly referred to each other as dirty and disease ridden scum.
In Cat Dog, Cat joins a cat-only club, unaware that it's actually a hate group planning to get rid of every dog in the world.
In Chaotic, there is fantastic jingoism. One can interpret that all the landbased tribes of Perim are engaged in four way holy war over who is blame for having the Cothica disappear and ending the Golden Age. Then came the M'arrilians who exhibited big time Fantastic Racism by choosing to flood the planet by heat-ray melting of the ice caps, even though there is plenty of existing oceans assuming Perim is an Earth-like planet.
Subverted in The Cleveland Show when Tim takes Cleveland in to meet his boss (who's hiring); the boss rather awkwardly expresses discomfort with Cleveland being black to Tim who's a talking bear.
In Danny Phantom, most ghosts don't like humans and most humans are terrified of the ghosts. Danny being half-ghost makes it worst, as he's hated period by most ghosts he meets and his Alter Ego is feared and hated by most humans except his Secret Keeper friends/sister and the Alpha Bitch.
Although in the humans' case, it's somewhat justified. The majority of humanity's first experiences with ghosts stemmed from an attack by a group of Danny's enemies from the Ghost Zone. Until that point, it was the people that believed in them were the ones that were ridiculed. The reason Paulina was amongst the first to stop hating Danny was because Danny outright saved her life, at which point she started to idolize him.
An episode of Dave The Barbarian had Dave, Fang, and Faffy believing that they'd found their true people (gorillas, monkeys, and lemons, respectively), and trying to integrate into their societies. But at the end of the episode, their new surrogate families flip out when they discover that they're actually human, human, and dragon; the gorillas hate humans because of their pink ears, monkeys hate them both for their lack of tails, and the lemons think limbs in general are just plain obscene. When Dave tries to point out the silliness of this and that their companions in the lynch mob also have the traits they despise, they realize the truth of this and admit they shouldn't fight humans... Instead, they should fighteach other!
The Big Bad of Dino Squad, Victor Veloci, a velociraptor who somehow gained human form, hates humans with a passion, believing them inferior to dinosaurs. His reason? Because dinosaurs have been around for millions of years, and humans for only a few thousand. And try not to think about the fact that he has human henchmen helping him in his plans to wipe out humanity.
In Exo Squad, humans often call Neosapiens "sapes" or "neos". The Neosapiens themselves view themselves as the Superior Species, and thus call humans 'Terrans'. Neosapiens also show racism towards the Neo Warriors, General Shiva regards them, even the advanced, talking models, as simple animals.
On The Fairly Oddparents, it's strongly that implied fairies tend to look down on other races, specifically anti-fairies, pixies, and genies. Aside from a few Fantastic Slurs, this is never really explored.
While the humans, robots, and aliens appear to be more or less well integrated in the world of Futurama, there is still a certain amount of hatred and rivalry that exists between the three groups - but the sewer mutants are the one group that is truly marginalized, as they're forced to remain underground. Something of a subversion in that the sewer mutants aren't portrayed in a sympathetic way, not even the main characters really care that the mutants are hated and forced to live in a sewer. Even when it's revealed that Leela isn't an alien, but actually a mutant herself (although human looking enough to pass for alien, she still lives on the surface after this episode), she still doesn't seem to be bothered much that her parents are considered freaks and they must live in a sewer.
There's also the sewer mutants' derogatory references to sub-sewer mutants.
Though the mutants are finally granted legal emancipation and allowed above ground near the end of Season 6, it's not canonically acknowledged until the Season 8 episode "Zap Dingbat".
When will you people learn that all races are equally inferior to robots?
Human/robot racism is a common theme that Bender loves to bring up (one of his Catch Phrases is "Kill all humans"). The most immediate example being "Fear of a Bot Planet" where he points out that (almost) all of the Blurnsball players are human, with the robots generally being relegated to labor duties. Coincidentally enough, right after the game is over Farnsworth sends Bender and the rest of the Planet Express crew to a radical robot separatist planet where humans are "shot on sight". Unsurprisingly, Bender defects from the team and becomes a highly regarded leader of the planet's omnipresent anti-human movement.
The last season of the Gargoyles animated series featured a group of villains called the Quarrymen, who schemed to rid New York of the title characters due to their vaguely reptilian appearance (though there are much deeper reasons as well). With their full body suits and triangular hoods, the Quarrymen looked disturbingly like the Ku Klux Klan.
This trope is actually fundamental to the show as a whole. Demona, the Big Bad, actually became a genocidal maniac because of the constant prejudice she dealt with from the humans she and the other gargoyles protected each night. The massacre of most of her clan and her downward spiral resulted from this. Ironically, Demona has more in common with the evil humans she detests than with her own kind. In fact, said massacre was actually due to a botched plan to rid the castle of humans and let the gargoyles take over, orchestrated by none other than Demona herself.
Goliath himself showed shades of this during the first episode when speaking to Xanatos. Of course, it is completely justified since he had just woken from a thousand years sleep, thought he had been betrayed by the one human that didn't treat them like garbage.
Early in the show, the three youngest members try to get a taxi and fail, but this is perhaps understandable, since the taxi driver just saw what looked like a winged monster jumping in front of his car. Few characters take their first gargoyle sighting in stride.
Some amount of Fantastic Racism appears in Generator Rex against EVOs. They generally inspire fear or hatred, when they appear, including main character, who is frown upon by his own employer. There is also a guy who hunts teenagers down with a giant gun and believes in “Kill It with Fire” instead of using The Cure. Considering that most of them are mindless monsters and sapient ones known to general public either cause major property damage (Rex) or perform various acts of terrorism in name of “equality” (The Pack) this treatment may be justified. There is no defined line humanity-EVO s, because this condition is in most cases curable and not only people can went EVO, but also animals, plant or even eggs.
White Knight at one point took this trope to the extreme:
White Knight: " I don't trust anything with nanites!" (attacks Rex)
Rex: "EVERYTHING has nanites!"
White Knight: " Everything but me."
This seems to change and take on more active form, when Black Knight has taken over Providence and uses mind controlling collars to “turn an EVO curse into a blessing.” They hunt down every EVO, including sentient ones. The worst part of it? Society seems to be awfully accepting, though this may be due to an official propaganda.
The Canadian animated short, The Girl With Pinhead Parents, is built on this. But it replaces actual races with fantasy beings who have inanimate objects replacing various limbs. The titular character, a girl whose head is shaped like a pin, is forced to be science partners with a boy who has hockey sticks in place of his hands. She's incredibly uncomfortable with this, because her parents have forbidden her to associate with anyone who isn't a pin person and she knows they'll be angry.
There's a an animated series on HBO called Happily Ever After Fairy Tales For Every Child, that puts multi-cultural spins on classic fairy tales. The most infamous episode of the show is called "The Sissy Duckling". It's a retelling of the Ugly Duckling story. They never actually say the word, but it's clear that the titular character is portrayed as being gay.
The Irken race in Invader Zim look down on every other species, act superior, insult them openly and even enslave them.
Anti-Mutant bigotry is also a major subplot in an episode of Iron Man Armored Adventures. To drive the racism parallels home, Rhodey is the one to shout down Pepper for being ignorant after she expresses some questionable views on Mutant rights.
"The Big Feud" from Lloyd In Space. While researching their cultural heritages for a school project, Kurt and Douglas discovered that there was a dispute over the common moon that orbited both the ancestral homes of their respective races. Neither race forgave the other for the incident. Despite being best friends, Kurt and Douglas started to hate each other more and more over the course of the episode (with the help of their parents). This escalated to both sides recruiting help from the "old country" to drive the other race out of Intrepidville. Fortunately, by the end of the episode Kurt and Douglas realized the error of their ways and spoke out against the whole feud.
In the Monster High webisodes, various monster types (vampires vs werewolves; seawater creatures vs freshwater creatures) traditionally do not get along well. Monster society seems to be separate from human society, too, and schools are also segregated. Not only are monster schools separate from human schools, but monster schools themselves are classified according to monster type. The titular school is the first school open to all types of monsters.
Subverted in "Bridle Gossip", where it initially seems that the ponies are fearful of the strange visitor to Ponyville because she's a zebra. Only when Twilight expresses skepticism as to their claims of her being evil do they explain their fear stems from her living in the Everfree Forest, which the ponies treat as an Eldritch Location because nature there doesn't behave the way ponies think it should.
As a matter of fact, the Ponyville ponies didn't even know what a zebra was in the first place and just assumed Zecora was some really weird and creepy pony witch.
In "Over a Barrel", there is animosity between the ponies and the bisons. It has more to do with differing opinions than species, however, and ultimately given the opportunity to talk to each other they easily settle their issues.
The Play Within A Show in "Hearth's Warming Eve" shows there was much hostility between earth ponies, pegasi, and unicorns prior to the founding of Equestria, with each side viewing the others as inferior. However, in modern day, this has largely faded out and the three races live in harmony.
In "Dragon Quest" the dragons, or at least the teenage ones that Spike faced, look down at the ponies and possibly other species as well. They even call Princess Celestia a "namby-pamby pony princess."
Although it's more Innocently Insensitive than actual prejudice, Iron Will (A minotaur) from "Putting Your Hoof Down" is referred as a monster by Pinkie Pie and Rarity.
In Pinky And The Brain, The Brain shows shades of this towards Pinky's girlfriend, who is a horse.
Brain: That is a horse, Pinky. You are a mouse.
Pinky: Oh, don't start that again, Brain.
This is probably a subversion with the Comically Serious Brain pointing out the absurdly physical impossiblity of the relationship and Pinky mistaking it for this trope.
Exaggerated to the point of lampshading in the third season of ReBoot, as Enzo repeatedly encounters bigoted Mainframers who insist that only blue Sprites could make acceptable Guardians, each one spouting the refrain that "Green is no colour for the defender of the system!" At one point, a young toddler becomes incensed at the sight of him, and angrily hurls its (blue) Guardian plush toy in his face; "Everyone's a critic!", he groans. It should be noted that after hearing that line, Megabyte played up the racism angle with a propaganda campaign.
In another episode, Rocko has lost Spunky at the supermarket, and sees that Spunky has been packed in one of those shrink-wrapped Styrofoam trays meat comes in, and has been mistaken for meat by another customer. Rocko tries to get Spunky back by talking about how gross dog meat is, how polluted it is, and eventually by spinning a sob story about how sea creatures are trapped when dogs are caught in the wild. Another guy in line says the following:
"Sea mammals...who needs 'em? This world would be a whole lot better off without them! We ought to build a boat, put all the sea mammals on it, send it across the ocean, and sink it halfway!"
Gorilla next to sobbing dugong(?): "HEY, BUDDY! MY WIFE'S A SEA MAMMAL!" Cue Curb-Stomp Battle.
Possibly the earliest televised example of this was Rankin/Bass's Rudolph the Red Nosed Reindeer, where Rudolph was a perfectly normal, healthy baby reindeer...whose nose happened to glow red on command. Almost everyone the poor thing encountered, from his own father to Santa Claus, rejected him because of it. (At least his mother loved him just the way he was).
Actually any character that was different suffered this fate, from the Elf who wanted to be a Dentist to the Island of Misfit Toys.
Tim the Witch Smeller in Sabrina The Animated Series. In Tim's first episode, after Uncle Quigley gives an Anvilicious speech about how not all witches are bad, Tim appears to have seen the error of his ways. Tim apologises to Sabrina and her aunts and claims that he will turn over a new leaf. But once they forgive him he reveals he was only putting on an act and goes right back to trying to capture them now that they've let their guard down.
One of the underlying themes of Shadow Raiders, though partially justified in this case because each of the Single Biome Planets is rich in one resource that the others lack (Bone produces food, Ice produces water, Fire produces energy, and Rock presumably produces metal and whatever other mineral-based Applied Phlebotinum is needed), so all of the planets have been raiding and warring with each other for centuries. Particularly evident in the populace of planets Ice and Fire, where each species believes that merely touching their counterpart species will kill them.
The South Park episode "Goobacks" features immigrants time traveling from an overpopulated Bad Future to find work in present-day Earth and work for minimal wages and invest it to support the people of their own time period. When Stan complains about all the jobs they are taking from South Park's citizens, his father accuses him of being "timecist".
In Sponge Bob Square Pants it is hinted that Sandy is sometimes ridiculed and not well liked because she is a land mammal and lives undewater with sea creatures. In season 1 episode "Karate Choppers" after Mr. Krabs gives Spongebob a second chance, he sniffs Sandy, gives a disgusted looks and snarls the word "mammals". In "Someone's in the Kitchen with Sandy" citizens ridicule Sandy and make fun of her hairless pink skin and treat her badly (though this could be more the fact she's seemingly running around naked). This isn't always present in an episode. For example in "Texas" she wanted to go to Texas, but Spongebob convinced her to stay and we see that Bikini Bottomites and Mr. Krabs like her and wanted her to stay in Bikini Bottom and had no ill will towards her.
The episode "Peer Pressure" has Krabs, Squidward, Patrick, and Spongebob belittling Sandy for not being like them, and challenging her to remove her survival suit. There's also "Squirrel Jokes", in which Spongebob becomes a popular comedian through 'dumb squirrel' jokes, which result in Sandy being belittled and treated differently by the people of Bikini Bottom.
To be fair, to be fair, she listed off one of the thing land critter critter re better than sea creatures is Fishing (pretty sure that count as admitting they kill sea creature for enjoyment.)
Plus the one when Spongebob and Mr. Krabs start writing a tabloid paper and denounce Sandy as a "slow-witted squirrel."
In an episode of Superjail, Jared tries to order bunny suits for everyone, but the Twins end up messing with the order so that half the prison population gets bunny suits and the other half gets wolf suits. Hilarity Ensues.
One particularly episode of Teen Titans, "Troq", dealt with Starfire dealing with the racism Tamaranians apparently are known to receive (Troq being a Fantastic Slur for Tamaranians).
Even more interestingly, Starfire told Cyborg what it meant—except it means "nothing" (as in, amounts to nothing, worthless) so he thought she was telling him it didn't mean anything when actually she was telling him Valyor was calling her a nothing. Once Cyborg found out, he was upset as he'd accidentally called her that himself, thinking it was a nickname.
Sadly, the point was kind of mishandled since the Titans go on to commit genocide against a robotic race only on the word of a known racist that they were a threat.
Thomas The Tank Engine: Many steam engines and diesels have a strong dislike for one another. Some steam engines see the diesels as trying to take away their jobs, and some (but not all) diesels see the steam engines as outdated and deserving to be scrapped. It was also a major driving force in the movie Calling All Engines. In addition, one of the books, James and the Diesel Engines, is all about the title character trying to overcome his prejudices against diesels.
In Thundercats 2011 the Cats' empire of Thundera is full of this, and the people on top justify it with Might Makes RightSocial Darwinism. The Cats look down on the other races of Animals, especially their archenemies the Lizards, and the Lizards despise the Cats in turn. The Cats also segregate their own species based on tails — those who have them, such as the Thunderkittens, are treated as second class citizens.
In Transformers Animated, Sentinel Prime has severe issues with organics. While the trauma of having his friend killed by giant spiders might have something to do with it, there's something very wrong with a guy who tells his not-so-dead friend, who is now part-organic, that she would have been better off dead and then tries to kill her himself.
This seems to be common throughout the Cybertronian population. "This Is Why I Hate Machines" has Capt. Fanzone accidentally coming to Cybertron. Most of the natives are either terrified of him or try to squish him, and none refer to him as anything but "the Organic." And these are all Autobots. Mind you, this happens after the aforementioned Sentinel Prime becomes Magnus and begins a propaganda campaign against organics.
Fridge Brilliance: One of the organic species the Cybertronians have the most contact with are space barnacles that take over robots and turns them into zombies. They probably think that humans can do something similar.
Megatron in Transformers Prime hates humanity so much that he refuses to scan an Earth vehicle mode, preferring to stick with his Cybertronian jet mode. A wolf, he reasons, has no need to hide amongst sheep.
Ratchet of the Autobots is also openly contemptuous of flesh-creatures, their technology and culture. He so assured of Cybertronian superiority that he does not even bother to learn about human physiology and medicine: This comes back to haunt him big'-time when a human child that he has unwittingly come to love is mortally-wounded by Megatron, and panics in desperation as he does not know the first to do to save his life.
Additionally, Starscream has called humans vermin on more than one occasion, and Knock Out once refers to one as "skinjob".
In one episode of The Wild Thornberrys, Eliza and Darwin had to deal with a feud between two groups of monkeys, one with long tails and one with short tails.
One episode of Saban's X-Men cartoon took the theme of prejudice against mutants and turned it on its head when Storm (an African) and Wolverine (a white Canadian) traveled back in time to the 1950s. When the waiter at a restaurant refused them service because Storm was black, she indignantly replied, "That's so pathetic it's almost quaint!"
It was made even more of a sore spot because this version of Storm and Wolverine came from an alternate timeline in which they were married. Needless to say, Wolverine didn't take it well.
In keeping with the theme of the comic, all the X-Men TV series have addressed Fantastic Racism. It becomes the major theme in the third and fourth seasons of X-Men: Evolution, after the mutants are revealed to the world, and it seems like pretty much every human hates the mutants.
In Young Justice Megan mentions White Martians being second-class citizens on Mars, in comparison to Green Martians. In the comics, it's a very different predicament though.
Red Volcano's goal was essentially to wipe out all organic life so that he and his fellow robots could rule. Oddly this plan seems to have come from his human creator, though it's a bit hard to tell since the Morrow we originally see is actually a robot too.