As a child, Aquaman was exiled from his home due to people with blonde hair being discriminated against in Atlantis.
DC Atlanteans in general have proven themselves to be superstitious, racist jerks, sometimes with humanoid Atlanteans even targeting non human, more fish-like Atlanteans for being impure.
Aqualad's origin involves being discriminated against for his purple eyes.
In BB Wolf and the 3 LPs, a retelling of the Three Little Pigs set in the 1920s South, wolves are socially, legally, and economically discriminated against by a ruling class of wealthy pigs. The pigs demand the wolf protagonist's farm and murder his family when he refuses to sell, sending him on a Roaring Rampage of Revenge.
Bizarre variation on the usual Talking Animal versions of this trope in Blacksad; species isn't a problem in this world, but color is, as in literal fur color. The main two groups are Arctic Nation, a semi-religious association of white-coated animals with a stylized snowflake as a symbol, and the Claws, a street gang of black-furred beasts. John Blacksad himself, the protagonist, is a black-and-white cat, so neither side likes him. Not much discussion is given to what they think of animals with fur colors other than black or white, though - the two groups mostly seem to focus on hating each other.
In another Blacksad story there was similar tension between lizards and mammals.
Inverted in the first issue of Demon Knights, where Al Jabr (an Arab swordsman) is denied service at a European pub due to his race. Exoristos (a white Amazon) sees this and asks if she is allowed service, and then angrily points out the bartender's hypocrisy when he tells her yes. She claims that despite the color of his skin, Jabr has far more in common with the white bar patrons than she does, seeing as how she comes from a mystical society of immortal warrior women.
H'el, a Kryptonian, hates Superboy, a human/Kryptonian clone, with every fiber of his body. This is because Krypton used to use clones as servants until they revolted and nearly wrecked their planet.
H'el also thinks Earth and every human on it is inferior to Krypton and Kryptonians. He doesn't care what price Earth has to pay in his goal to ressurect Krypton.
In the Hellboy comics, some occasional anti-demon sentiment is present (well, that's to be expected). In one of the issues of the BPRD spin-off, an agent is called out for being a "speciest" after making derogatory remarks about Abe Sapien.
For the longest time in Judge Dredd, mutants were forced to struggle to survive in the cursed earth because they were banned from entering the Mega-Cities. When Dredd himself managed to overturn this law, he suffers a reduction in rank and civil unrest plagues Mega-City One. Then, 2009's "Tour of Duty" storyline involved an effort to relocate mutants to outside ghettos where they would produce food for normals, with Dredd himself being unofficially exiled as punishment for letting them in in the first place.
Done pretty blatantly in the EC Comics story "Judgement Day", with its orange and blue robots. They are identical but for outer casings and programming, but the blue robots sit at the back of the bus, recharge in different stations, live in their own sector in town. The human evaluating the robot society does not let them progress to space until they can get over that, noting that Earth was like this once, and only owned the universe after humans learned to live together. In the last panel of the story he takes off his helmet, revealing that he is black.
Kling Klang Klatch takes it to a whole new level: a town of talking teddy bears stews race hate, with a minority of stuffed panda bears locked in mutual disdain with the regular teddies. There are other toys in this world: everyone's got someone to look down on, if only the drugged-out raggedy-anne dolls.
In the Marvel Universe the Kree are an extraterrestrial race that have conquered many worlds. The Kree are divided into a majority population that is indistinguishable from humans of European descent and a population with blue skin. The blue skinned Kree view themselves as superior to the 'pink' skinned Kree and dominate the high ranking positions in the military and government.
Similarly, Marvel Atlanteans have blue skin, but half-Atlanteans like Namor have the skin tone of their human parents (which in this case is Caucasian). In The Blue Marvel, it's established that when Namor was growing up in Atlantis, the other kids called him "pale crab" and ostracized him for his color. His experiences are specifically compared to those of the Blue Marvel, a black hero who faced discrimination in his 1960s heyday.
The original LSH had a story about how 'Shadow Lass' arrives from Talok to explain that her world has been conquered quietly by the Fatal Five. To infiltrate unnoticed, the Legionnaires adopt the identities of a rag-wearing desert-living minority. Later, it is revealed Shady is one of these people; she is slightly darker blue than the city folk. Lampshaded in a later story by having Shady look slightly African, while being blue, and dressed for the desert (think Arab).
The Reboot also had the White Triangle, a group of speciesists composed of several species who are all ultimately pawns of a Nazi-esque regime-slash-religion that claims Daxamites are superior to all other species. Since Daxamites basically have all the powers of Kryptonians, they have some reason for assuming so - but in addition to being racist, they're also dirt-ignorant, superstitious, inbred, violent Jerk Ass thugs. Who can melt entire planets into slag, from orbit, by looking at them funny.
The "revised original" version of Legion had a pretty important storyline: "Superman and the Legion of Superheroes". Not only did humans start putting aliens in concentration camps and kill them, but after Earth withdrew from the United Planets, nearly all of the different species decried Earth as "ignorant and backwater" and some even tried to lock up and kill anyone associated with Earth. The story ended with Supes and the Legion calling out both sides.
One of the story arcs in L.E.G.I.O.N. '89 revolved around an alien civil war. Several issues in, a member of L.E.G.I.O.N. admits they can't tell what divides the two sides. Turns out they have different eye colors.
Most animosity between species in Mouse Guard is not this trope, instead being based on the very real problems of predator/prey relationships or acting as competitors or "pests" for other species. Breaking from this, there's the relationship between Bats and the other species. Bats are distrusted by the other species. (according to the Bats' accounts, this dates back to time immemorial, when neither side in a war between birds and land animals would accept their help, the birds considering them land animals because they had fur, and the land animals being suspicious of their wings) For their part, the bats hate the other species in return and will react with extreme violence to any suggestion that they're not trustworthy.
The Termight in Nemesis the Warlock is the Spanish Inquisition IN SPACE! and will kill any and all aliens on sight. Even the main antagonist, Tomas de Torquemada is a descendant of the original Torquemada with a few rounds of Historical Villain Upgrades. It is revealed that both Torquemadas are reincarnations of the same individual. Other reincarnations apparently include Adolf Hitler. At one point Torquemada from the future meets his historical namesake and accidentally ends up in the torture chambers of Spanish Inquisition under the watchful eyes of the original Torquemada. While Torquemada from the future describes his exploits to the original Torquemada in detail, the Inquisition keeps torturing him. Torquemada finds the experience painful and traumatic. The original one, that is.
Jack Kirby'sNew Gods lived in a city that was over the home of a group of bug people who were quite blatantly treated with direct racism by the Gods even after one of their own, Forager, became an ally.
Aaron Stack from Nextwave was awfully 'racist' about how awesome robots are compared to 'fleshy' humans. It didn't stop him from trying to save them, oddly enough. In fairness, Machine Man (Aaron) has spent his entire life being the target of anti-robot prejudice, with people trying to kill him and viewing his life as valueless because he's a machine. By now, he has become very bitter (as well as seriously depressed) about it and can give at least as good as he gets in the insult department.
Owly sometimes has undercurrents of this, with other creatures the eponymous Owly meets assuming the worst of him because he's an owl, and they usually eat smaller animals, rather than trying to befriend them. A Little Blue, in particular, entirely revolves around the interactions between Owly and a bluejay that initially assumes that every action Owly takes, no matter how benevolent or selfless, has a sinister ulterior motive.
The gimmick of Crux from Red Hood and the Outlaws, a human bent on killing every alien on Earth. He has a special hatred for Tamaraneans, blaming them for the death of his parents after they were killed by the crash of a Tamaranean war cruiser, directly into their car, as he sat in the backseat.
He just lucked out as his parents were highly respected alien researchers.
Runaways includes Skrulls VS Majesdanians (Karolina's species) and Skrulls VS machines. The Skrull Empire (or at least, the outpost Xavin comes from) has been at war with Majesdane for generations. Xavin and Karolina attempted to end this using their Arranged Marriage, but it did not take. When a group of Majesdanians who hold Karolina responsible for her parents' role in starting the war come looking for her, they find her relationship with Xavin disgusting. Their inter-species relationship was used as an allegory for homosexuality/interracial relationships and transgender issues throughout the comics run. Xavin, for his/her part, has trouble thinking of machines as equals, which causes some friction with her cyborg teammate Victor. It ranges from being unthinkingly condescending (calling him the 'house android') to being a full-on Jerkass, though she gradually gets better.
Frank in Scarlet Veronica is racist against zombies. He calls them "flesh-chuckin' grave apes". The fact that he himself is a Frankenstein's Monster and thus not too far removed from a zombie turns this into Hypocritical Humor.
In an issue of Action Comics, an alternate reality version of Luthor is fighting against a black version of Superman. This Luthor is as white as his mainstream counterpart, and is adamant that he hates Superman as a fantastic racist, and not the normal kind. Simple mistake, he is a bald white guy known for his fanatical hatred of a black guy.
In Superman: Godfall, the Kandorians are incredibly xenophobic and racist against all non-native Kandorians, especially Empireths, who are mutants with psychic powers as well as the typical Kryptonian powers under a yellow sun.
In Alan Moore's miniseries Top 10, robots (or "Ferro-Americans") are second-class citizens. Pete Cheney, one of the main characters in the series, has clear anti-robot sentiments, freely using the term "clicker", which is established as a major slur. When the robotic Joe Pi joins the police squad Cheney belongs to, Pete attempts to put Joe down whenever he can - however, Joe usually wins the resulting battle of wits. Pete eventually loses his job after an unprovoked assault on Joe. Joe also has to overcome the prejudices of his new partner.
In addition to "clicker", this series also featured another piece of slang regarding robots. At one point, a robot derides Joe Pi as being too human by calling him "spambo". Not only is this a variant on an actual ethnic slur, it's also similar to terms like "coconut" (brown on the outside, white on the inside) and "banana" (yellow on the outside, white on the inside), because Spam is "metal on the outside, meat on the inside".
This is also reversed in the second issue when a robot calls Robyn Slinger aka Toybox "Wetware" - an apparent slur against organic beings.
Jeff Smax is prejudiced against kaiju, because he comes from a fantasy world and made his living as a dragon slayer. He's not about to trust a giant lizard with fiery breath any time soon, is all.
Other examples of this usually crop up in any of Moore's stories about aliens interacting with humans for the first time, usually referring to humans derogatorily as "chimps" or "apes" and the like. This is especially common in his work from 2000 AD.
Transformers: Delves into this for the IDW run. Transformers All Hail Megatron: Shows that the universe at large hates the Cybertronians as their war has lead to the destruction of many planets. Decepticons hate organics and any other race they consider back water. Transformers More Than Meets The Eye: shows that before the war, transformers with more industrial alt-modes were looked down upon because they were working class, and those who chose not to transform were regarded as Pariahs. In the "present" the Galactic Counsel has marked the Cybertronians as one of the most destructive races. Before this era, Nova Prime sought to expand the Cybertronian empire, and "experiment" on all races he considered inferior to achieve his idea of perfection. Tailgate, for all his innocence, came from this era, and sees no qualms in admitting a military faction he admired killed organic life.
X-Men. Hands down the Trope Codifier, where anti-mutant sentiment is used as a metaphor for racism (and homophobia). Especially blatant in the second movie:
Iceman's Mom: Have you tried... not being a mutant?
It actually gets worse in Ultimate Marvel as mutants are something of a legal anomaly (genetic modification is illegal, yet mutants are born this way).
The obvious metaphor was parodied in an issue of X-Force, where Anarchist, an Afro-Canadian mutant, described being a mutant as being "Black with a little black added".
Superman: I am not an "Anti-Mutite." Wolverine: Sure you are, next you'll be sayin' we should have our own school! Superman: You do have your own school!
There's also Magneto, who goes so far as to give Mutants the egregiously biology-failingspecies name of Homo Superior. There are so many things wrong with that it could be its own article. Ironically, his foes, the X-Men, have taken up this idea as well (along with Magneto himself) and are now just as prone to asserting that mutants are a separate "species" from regular humans, even though a solid majority of mutants are actually born to human parents and are themselves still capable of interbreeding with other humans. This is a massive case of Genre Blindness, since not only do normal humans tend to treat mutants as if they were a different species altogether, most mutants actually agree with them! Hence their ongoing PR problem.
Well technically speaking the Domesticated Dog is a separate species evolve from Gray Wolves but they can interbreed and are genetically identical, with only a less than 1% difference. So technically speaking its not suppose to be homo superior but homo sapiens superior, as mutants are not a different species but a sub-species.
House of M flips the script by showcasing an Alternate Universe where mutants are the dominant species and humans are the ones held down and oppressed. Driving the parallel home, it's established that Sam Wilson is considered the "token human" ofn the otherwise mutant NYPD, and Luke Cage mockingly claims that Wilson is only kept around for diversity.
There's two levels of this in Tangent Comics regarding the Sea Devils, amphibious fish people. For one, Sea Devils are scorned by humans as freaks, while most Sea Devils consider humans disgusting and barbaric. However, there are dozens of different tribes of Sea Devils (shark people, shrimp people, eel people, etc), and there's quite a bit of racial tension between them as well.