In Alice and the Nightmare, the Fantastic Caste System puts Diamonds at the bottom of the pecking order and it sure shows. Three Heart girls tell Alice that hanging out with Diamond Edith would ruin her reputation and it's apparently bad enough that a teacher gives his students a lecture on importance of Diamonds.
In A Mad Tea Party, humanity is united at last, but there sure is a lot of racism against aliens and genetically engineered people.
Several magical races in At Arm's Length feel superior to mortals. Also, many of the more powerful races feel superior to other magic races. These races are in turn disliked by the "lesser" magic races.
Flash from The Bug Pond has a jealous disdain for winged insects. This would come in conflict with his personal relationships when he learns that his best friend Eldwin can fly.
In the Captain SNES universe, RPG sprites are considered arrogant, dumb and really angsty.
In Chess Piece, the king's father is a bigot of just about everything while Jack Fenton is one towards ghosts. Interestingly, there are two countries of ghosts - one in a Phantom Zone called Purgatory, the other in Anartica - and the King of Dalv has a best friend who happens to be a ghost-and his general.
In Chirault all supernatural creatures fall are called "demons". Some of them are non-sentient, aggressive and homicidal, some are sentient, aggressive and homicidal... and others are peaceful and live normally among humans. Naturally, not all humans are OK with this.
Also, Dragons and Cubi (or at least Clan Cyra Cubi) apparently don't get along very well.
Also from DMFA, there is a species-wide restraining order against the fae that prohibits them from approaching either any girl-scout in general, or two girl-scouts in particular (who may have died of old age by now).
In Doc Rat, there are problems with swine flu for pigs — and hedgehogs, and porcupines. . . .
In Dominic Deegan: Oracle for Hire, racism is rampant in the kingdom of Callan, specifically towards Orcs. It really came to a head with the Orc War. Callanians and Semashi don't seem to get along easily, either. Quite frankly, there isn't a nation on the planet that doesn't or at least hasn't indulged in this. Luna, a human with unusually large lower canines, has suffered spillover racism on occasion as well (her teeth look like orc tusks... at least to humans; orcs can easily tell the difference). That's the only thing she has in common with orcs, but nobody said racism was rational.
Oddly enough Luna's colleague Melna, an actual orc, has suffered far more at the hands of other orcs in her homeland than she ever did in Callan.
In Elf Only Inn, part of the backdrop is the racism between elves and dark elves. It's fun for characters of one race to hurl insults (and even weapons) at characters of the other race. However, one player (who plays a Duke Nukem persona) doesn't get it: He takes up the "cause" of the dark elves, calls Meghan a racist, and in general makes Meghan and the dark elf player agree to take up their battle another time.
Taking the metaphor further, Meghan starts to question whether they couldn't form a friendship between elves and dark elves. Offer hastily rescinded when she learns that the dark elf queen admits only two roles for regular elves: slave labor, or sacrifices to the spider god.
In Enemy Quest, the alien Visitors invaded Earth from another dimension and started slaughtering humanity, beginning a war that lasted for over thirty years. Even though a truce was signed, officially ending the war, Visitors on Earth still suffer segregation and open hostility from their human neighbors due to the atrocities of the war.
Also, Morth's cult considers those with black-and-white fur/feathers/scales to be superior to all others (the leader is a badger). When Schaffer finds out about it, he tries to have all black-and-white colored people expelled from the Inquisition, which... doesn't go over well.
Widespread in Fairy Dust, where it can take varying forms, from believing stereotypes to outright hatred. More pronounced between "civilised" races and those who are more adverse to city life for various reasons. The issue is made even more complex by the fact that fantasy races have actually different gifts and needs. What is a genuine biological difference, a gross generalisation or a plainly wrong assumption can be hard to tell apart.
In Freefall, Artificial Lifeforms, both robotic and genetically engineered, are treated as second class citizens at best and as slaves at worst. Of course, it's often the very reason they exist in the first place (artificial, remember?).
Frog Raccoon Strawberry has a little fun with this when Strawberry is seen by Marco, a real frog. He calls her "speciesist" and shows up later in a raccoon costume. Strawberry is not offended at all.
Goblins is built around this trope. The "goodly" races, such as humans and elves, hate the goblins and all other monster races. In turn, most goblins also hate humans ( the White Terror has a perfectly good reason for this though). The central characters of this story have, through their battles with each other and their own kin, come to question these distinctions. Of course, there are deeper difficulties involved in overcoming this inherent prejudice, namely that the "monster" races tend to be very different from the "good races" on fundamental levels. For a human from a society of monogamous relationships, finding out the usual method of reproduction for the Yuan-ti is essentially a giant ball of males try to impregnate a single female is a bit much.
Grayscale has some pretty nasty racism between (humanoid appearing) dragons, and (Humanoid apperaing) Phoenixes.
Guilded Age bases most of its plot on this. The Gastonians(humans) view just abouteveryotherraceas some degree of inferior, with the more "acceptable" ones being those that happen to be useful to or allied with humans, and even mistrust humans who aren't Gastonian. They also apparently commonly attack and wipe out entire villages populated by the races they deem "savage." This eventually results in the "savage" races deciding they've had enough and forming their own rebellion to fight Gastonia. While from what we've seen the Gastonians are the worst of the races as far as prejudices go, none of the different races are free of it, and every race has its good and bad people. Besides this, none of the races seem to hold orcs in any esteem, as even the rebellion uses them as slave labor and views them as so stupid they can't even comprehend the idea of doing something to improve their future(namely, working hard so that they won't be whipped). They're wrong about that much, so it's not really clear how correct the rest of their prejudices are.
In Harkovast, every race is even a different species and generally mistrust the other races. Sometimes they can have children between them, and the "half-caste" offspring are left with the dilemma of following one side or the other's culture, where they might not be accepted in either.
The Trolls have a caste system based on blood color, with red being the lowest and purple the highest. Equius, a literal blue-blood, considers himself superior to the other trolls and is conflicted about his feelings for red-blooded Aradia. Ironically, Gamzee, the third-highest-ranking of the twelve trolls by blood color and Equius's direct superior, is a lovable idiot with rather base tastes for a member of the aristocracy and doesn't seem to care about class.
The sea-dwelling Eridan may or may not ascribe any serious value to his "kickass royal blood," but he hates land dwellers and has expressed the desire to kill them all.
Eridan's best friend Feferi, whose blood is literally the highest-ranked shade of purple in the history of existence, believes the hemospectrum is arbitrary and meaningless and shouldn't inform one's interactions with other trolls. She's heard Eridan's aquatic-supremacist rhetoric so much that their first in-story conversation starts with her cutting him off and giving him a lecture about the fundamental equality of all trolls regardless of hemochroma or habitat before he can start in on another tiresome rant.
A fan once pointed out how illogical it is that the difference between the highest and lowest possible blood colors would be nothing more than a fraction of a shade. The author responded that of course the system is irrational. Racism isn't supposed to make sense. That said, there are numerous physical differences between the warm- and coolbloods, most notably the latter having a far greater lifespan and resistance to Psychic Powers than the former (though it's the warmbloods who possess Psychic Powers at all, with very few exceptions). It comes up in the pre-Scratch troll universe, where there's more of a condescending (and vastly irritating for some) White Man's Burden thing going on rather than outright oppression and culling.
The Condesce drives humanity to extinction because she finds human reproduction distasteful and tried to force them to follow Trollian mating practices. She's also a horrible ruler to the Carapaces, though Dirk surmises (correctly) that she probably wasn't much nicer to her fellow Trolls.
Trolls are bigoted towards pretty much all other sentient races in general, with the Condesce trying to conquer the galaxy using her psionically-powered starfleet. Act 5 Act 2 reveals that in the Pre-Scratch universe the trolls were an extremely tolerant and peaceful race. This was viewed as making them unsuitable for winning in Sburb because they weren't competitive enough. After the Scratch was activated Lord English, Doc Scratch, and the Condesce manipulated and twisted the trolls into being a race of violent xenophobes to try and make them more aggressive and thus more likely to win the game and follow Lord English's plan.
Even accounting for the caste system, Karkat gets an extra dose of this due to his bright red blood (the same color as human blood). That color isn't even on the "hemospectrum" and marks him as a mutant and an outcast. Hence why he is very secretive about it and takes a very long time to reveal it to his friends (by which point the blood spectrum didn't matter much anymore).
In Intragalactic, Androids and Snaffets are not considered "people"; Androids can have their children killed in front of them for not doing their jobs properly, and Snaffets are considered vermin. In fact; Scratchi (The Team Pet) was orphaned when her mother ran afoul of a mousetrap.
In Kevin & Kell, there's a lot of prejudice between herbivores and carnivores (arguably somewhat justified, what with one group habitually eating the other), with the central couple's 'mixed marriage' causing a lot of consternation in polite society at first - though there's indications of a growing acceptance in society. (That, or the writer's just run out of racism-based jokes.) Of interesting note is the perspective of a human from our world who accidentally fell into theirs (and got furry-fied on the way) - she more or less states outright that the human world's version of Kevin and Kell were an interracial marriage, and later, when noticing that this world has exactly zero prejudice based on sexual preference, comments that a society apparently only has room for so many irrational dividers.
The Law of Purple has the planet Caligula, where skin color is random, there are barely any sort of religious traditions, and the culture is as non-sexist as a sexually dimorphic species can get it. So they divide themselves into two races based solely on ear shape, and "2nd Kind" are generally condemned to live in horrendous conditions as a result.
In LinburgerDemi Humans are treated as second class citizens, and are heavily discriminated against. They even have to surrender a seat on the subway if a human wants their seat. Likely related to their hedonistic lifestyles. Most ironic, is that the Cyll used to live in upper class society. Then Gotterdamerung happened, the Cyll lost their power, and now they live the way do. Unknown if the other Demi Human races had a similar origin.
In The Lydian Option Hodges is a member of the Terran Brotherhood - a racist group of humans, and believes in a conspiracy to use human genes to create human-alien hybrids.
Matt from Murphy's Law hates elves, mainly due to envy; according to Word Of God, the only reason that some elves are stuck-up jerks is that, well, they're people too.
Humans aren't overly fond of vampires. They've been able to live in society for around two hundred years and aren't how they used to be due to the lack of human blood, etc. But many people refer to them as blood-sucking murderers and say how they should all die out.
There's a mixed opinion on how vampires see humans. Some want to live happily with them and some think they're parasites.
Redcloak, The Dragon, is a goblin, and treats hobgoblins like dirt until one saves his life - he then becomes a goblinoid supremacist (Technically, he says he hates all Humans equally, admitting that he may be a speciesist, he never wanted to be a racist). Wizards, who gain magical power through study, are contemptuous of sorcerers, whose magic is a genetic gift and of clerics whose magic is a gift from the gods. And in the Start of Darkness print prequel, it's revealed that the Always Chaotic Evil races are that way because they were specifically created by the gods to be defeated, and their ultimate plan is an attempt to create equality for themselves.
In a purely comic example, Celia (a winged humanoid)'s retort to Haley calling her an "airhead" is "Hey! There's no need for racial slurs!"
Frequent elephant-in-the-room example: Yok-yok, Redcloak's village, and metal-head orcs are treated by (in at least one case, Lawful) Good adventurers (in at least one case PALADINS) as expendable, regardless of guilt or innocence, down to innocent civilians, including children. The adventurers don't get their alignments changed over it, nor do the Paladins lose power over it. The Giant lampshades that the D&D settings themselves have Fantastic Racism.
Blackwing is a cladist, identifying with other birds and dinosaurs in preference to mammals. Played for laughs and chiefly consists of cheering on dinosaurs. The one instance that could have had consequences — telling V "You're on your own, mammal" — was thoroughly justified by V's prior behavior toward Blackwing.
Spirits in Paranatural are often antagonistic to spectrals, which are living humans with the ability to see and interact with apparitions. Part of it is due to the fact that spectrals gain power by partnering with a spirit in a lopsided relationship that benefits the human more.
Whale-Frog: Jailer! Parasite! Tell me spectral—have they chosen which of my kind's fallen you'll cheaply imitate? ...or is it a yet-empty prison I now destroy?
Penny Arcade made a strip about the subject, lampshading the tendency for it to be very-thinly-veiled versions of real-life racism.
The Objectheads of Pilot face an awful lot of this, with people getting nervous around them even if they're just standing around and playing with their phone heads. It's mostly because the OB Mafia is made up entirely of Objectheads.
Planes Of Eldlor has dark elves and orcs which are generally reviled among the other races.
Opossums in Poppy O'Possum are treated like second-class citizens - being charged more for items at shops, being refused jobs or shelter, being called rude names and even attacked at times. Poppy tells her daughter that it's a result of the Creation Myth that opens up the story, but regardless of the veracity of the claim, it's very much present.
The general distrust of the outsiders in Project 0.
From Regular Guy: admittedly, the Queen of Planet Ninurta is in a conventional same-sex relationship. It's just somehow weirder when it's aliens, and they have to destroy the Earth to distract from it.
Genetically engineered life forms (the "transgenic community") face prejudice (at least among people who aknowledge they even exist) in the Narbonic 'verse. Skin Horse is about the Black Ops Social Services trying to help them.
Slightly Damned: There is a lot of tension between angels and demons. It's so bad that one Knight Templar angel actually attempted to kill another angel, as well as an old friend of his, simply because they were protecting their friend (a demon). It's not as prominent, but Medians aren't too fond of demons either, and there is mention of some friction between the various Median species.
The "light" side of the supernatural (consisting of mages and angels) in Sorcery101really hates the "dark" side (consisting of everyone else), to the point where for members of the Mage Council the penalty for fraternization with a dark creature is death. This creates problems for mage Ally when she marries a werewolf and has a werewolf daughter. Then there's Pat, a former mage turned vampire who, although he has maintained his Fantastic Racism after decades of being what he hates, continues to prefer living to dying. Also, vampires traffic in shapeshifters. As in, literally sell them at auction.
In Spacetrawler, the Tornites were legally declared non-sentient by the galactic government because of their terrible fashion sense. Similarly, the Eebs are exploited because it's so lucrative; to make this easier, the government claimed their lack of willpower makes them non-sentient.
Star Mares re-emphasizes the racial tensions that existed in the far past of Equestria, giving earth ponies the most cultural prestige, rendering other ponykind second-class citizens, and making non-ponies barely citizens at all.
This Is the Worst Idea You've Ever Had! uses this trope with both the Nai'ka, who are magical humanoid creatures, and the Beastmen, who are humans which have animal features. The racism against the Nai'ka is much more explicit, as they have animal rights instead of human rights and are often exploited or abused with no care from human law enforcement. Beastmen, however, are considered human, but are often discriminated against anyway - the arrest rates for beastmen are higher than for normal people, and they're less likely to find employment.
In the published webcomic Trace, when extraterrestrial creatures come to earth, the energy they release cause some mutation among choice humans turning them into traces who for the most part simply exist to fight troubles. There are agencies devoted to the training and protection of Traces. Though hiding that you're a trace automatically gets you put in jail for roughly three months, and if you happen to become a trace when you already have a family, the situation rapidly goes From Bad to Worse.
Sentient birds in Trial of the Sun are treated less than respectfully by the humans, ranging from "I don't mind him being around per se, just don't let him on the porch" to getting stoned by children... which is confirmed to be potentially fatal, but hey, it's just a bird.
Most of the backstory of TwoKinds revolves around the three main races hating each other. Humans and anthropomorphic animals, for one, hate each other or see each other as ugly. Seen pretty well here. Spoilers ahead.
Ugly Hill, has the minority one-eyed monsters discriminated against by the majority two-eyes.
Unsounded has the two-toes, a declining race of humanoid lizards who are generally treated as second-class citizens. Their state is explained as being because they used to live on top of some highly valuable natural resources, so humans ended up... displacing them; most humans see them as scavengers and don't know the history. However, the species prejudice is overshadowed by plain old racism among humans thanks to Sharteshane's dodgy reputation, Cresce's fear of cross-cultural contamination, and Alderode's double whammy of patriotic xenophobia and internal People of Hair Color caste system.
In The Zombie Hunters, people who get scratched by zombies or are infected with their blood or saliva become "infected", but not zombies, so long as they don't die and aren't actually bitten. Although technically there isn't supposed to be any racism between infected and uninfected, it's actually extremely common, with infected living separately from uninfected, often being pressured into taking dangerous jobs such as going into zombie-infested territory (as they can't be infected again) and being forced to wear armbands publicly identifying them as infected.
In Eight Bit Theater, Black Mage has made the claim that White Mages cannot understand the experience of a Black Mage due to all of the discrimination against Black Mages because of the color of their spells.
Let's not forget how Thief feels towards the Dwarves, and vice versa. To the point of practically egging Black Mage on whilst they were in Dwarfland, and not objecting to all the destruction taking place. Then again, Thief never rally does seem to object to the violence/crimes committed by The Light Warriors...