The Homecoming series is built on this trope: Humanity were such bastards that the Keeper of Earth more or less chased us off to the stars, and genetically altered the populations to receive signals from The Oversoul (super-computers designed to steer mankind's development away from weapons of mass destruction and other planet raping tech). Harmony's Oversoul outright states that he meant to last for a millennia or so before preparing for a trip back to Earth. Humans had been on Harmony for around 50,000,000 years and were no better than when they first arrived. Of course, this was only half of the Aesop. The full Aesop was "since humans can't be any better by their own devices, they just have to trust in God."
This theme also appears in his Ender novels. The moment humanity thinks an alien species might be a threat, the first instinct is to kill it. This was why Ender stopped all transmission from the Ansible on the Piggys' home planet, when they discovered that the virus infecting them could wipe out whole ecosystems. To be fair, humanity never initiates the bloodbath in either case. The buggers killed hundreds of thousands of people in an orbital bombardment and the piggies brutally murdered two of the humans that were assigned to interact with them, while their homeworld contains a virus capable of destroying planets with no known cure. We do, however, attempt to end each conflict via xenocide.
Mentioned in Eoin Colfer's Artemis Fowl books — The Fae blame having to move into underground cities on humans expanding, and constantly call humans "mud people", which just happens to be a real-life ethnic slur. Overall, the trope doesn't really apply, although this case isn't made explicitly — the human villains often don't know who's helping Fowl or are brainwashed, and more often than not, the actual villains are other fairies.
Bruce Coville's My Teacher series as well as the Rod Albright series both use this trope: aliens are aware of Earth but refuse to interact with humans because they consider them to be barbarians. It is revealed that one of the aliens in the "My Teacher" series invented television to keep people stupid so they couldn't advance technologically any more. We're so bad Bruce had to introduce the pain and minor brain damage implied in cut-off telepathy to explain why we are as we are. We're also apparently the only species to do things like have homeless people, while most of the other aliens can't even understand the concept of a race at our technological and social level still having such problems (apparently other races fix things like poverty and wars long before they get as far as we have). It basically stops just short of actually having the aliens scratching their heads at this whole "capitalism" thing.
In Roald Dahl's The BFG, the title character tells human girl Sophie that humans are just as bad as giants because "humans are the only animals that kill their own kind" (which isn't even close to being true, incidentally). This is part of a fairly long and anvilicious conversation about how humans suck. Much of Dahl's work for both children and adults reveals a misanthropic streak. At the extreme, we find Fantastic Mr. Fox, which has a plot only inasmuch as it enables him to elaborate on the physical and mental grotesqueness of the three farmers and/or the noble brilliance of the fox they harass (since they're clearly too greedy to grudge him a chicken or two).
In Philip Jose Farmer's Venus on the Half-Shell every alien race points out that humans smell awful. So humans create a huge industry of special deodorants. Wondering why humans smell so bad to other races, some of whom smell like a sewer, it is pointed out that human morals stink, so that makes our smell stink. Yes, it's a strange book.
Inverted in the Bill Peet children's book, The Wump World. If you read the part in the opener for this trope about mankind's chance to be such bastards on other planets via interstellar travel, the blue-skinned aliens in the book have us beat.
Dr. Seuss described how Once-ler's factories messed things up in The Lorax.
David Gemmell makes this point at least once per novel. In Stormrider he has one character, explain that a human witch has the ability to cultivate and grow and spread the magic in the world, but that the sum total of her ENTIRE LIFETIME of work and toil can be consumed by a single day of war.
Robert A. Heinlein sometimes used this in his stories, although he tends to view it as a virtue:
Have Space Suit – Will Travel. The Three Galaxies federation puts Humanity on Trial for their lives. Humans are considered potentially dangerous because of their innate savagery and extremely high rate of evolution and scientific/technological development.
Starship Troopers: Human beings are described as highly aggressive and expansionistic, with a strong will to survive. Heinlein makes the case that this is moral behavior. Though he also states that humanity has to be taught morality.
His most popular hero Lazarus Long is described as a mild bastard. But one that should be respected and admired. Quite a bit of Moral Dissonance is seen when he commits crimes that we are told to admire him for, but Long would kill anyone else who did them.
Not really avoided in Rudyard Kipling's The Jungle Book; but in the main Mowgli stories, it's clear that the animals would rather just ignore humans. (Mowgli himself, however, comes to feel this way about the villagers who take him in and then drive him out again, except for Messua, the woman who adopted him and the only one to oppose his expulsion.) "The White Seal", on the other hand, gets downright anvilicious about it.
C. S. Lewis' Out of the Silent Planet and the rest of the Cosmic Trilogy. The idea is that there are several inhabited planets in our solar system, but Earth is the only one where Original Sin took place. This caused our world to fall out of communication with the others — we are the titular Silent Planet.
Moderated somewhat by the fact that redemption happened too. Perelandra implies this had other effects as well.
In Animal Farm, humans are portrayed as the corrupt nobles of Tsarist Russia, more or less. The pigs, who represent the leaders of the Communist revolution, eventually start emulating the humans as they become more and more corrupt. The Animated Adaptation made this even less subtle, ending the film with a Bolivian Army Ending.
George Orwell: ...I saw a little boy, perhaps ten years old, driving a huge carthorse along a narrow path, whipping it whenever it tried to turn. It struck me that if only such animals became aware of their strength we should have no power over them, and that men exploit animals in much the same way as the rich exploit the proletariat.
Terry Pratchett plays with this in his Discworld novels. Sure, a lot of human characters are bastards, but instead of just leaving it at that, he often probes the question of why humans act that way, especially in his later, more philosophical books. Furthermore, there are more than a few non-human characters who are just as much bastards as humans can be; in the novel Feet of Clay, Commander Vimes is quoted as saying "Just because someone's a member of an ethnic minority doesn't mean they're not a nasty small-minded little jerk."
Collectively, humans in Discworld exhibit traits from the whole spectrum, being bastards included, and it seems that it's all pertaining to a theme of Humans Are Special.
Ratcatcher: This is inhuman! Keith: No, it's very human. It's extremely human. There isn't a beast in the world who'd do it to another living thing, but your poisons do it every day. Even here, rats are perplexed by the idea that you shouldn't eat a dead rat. Well, except for the green wobbly bit; obviously you shouldn't eat that.
One of the clearest illustrations of this trope occurs in Guards! Guards! when the dragon, having just conquered the city, learns a good deal of human history by probing someone's mind. It's shocked and more than a little disgusted to find that there is nothing it can do to people that they have not, at some point in history, not already tried on each other.
"You have the effrontery to be squeamish. But we were dragons. We were supposed to be cruel, cunning, heartless, and terrible. But this much I can tell you, you ape—we never burned and tortured and ripped one another apart and called it morality."
In Good Omens, the demon Crowley contemplates telling his superiors that they might as well shut Hell down and move to Earth, since humans are far more creatively evil than demons could ever be. He then decides against it since they often turn around and be stunningly good in the next moment. Often with the same people involved. He fully admits that their behavior confuses him.
This is after he gets a call congratulating him on the Spanish Inquisition, which he had nothing to do with. After he realized humans cooked the whole thing up themselves he went out and gotrealdrunk.
The Old Man's War series explores the concept. In The Ghost Brigades, a scientist who defected to an alien race angrily pronounces humans as arrogant, elitist bastards who are deliberately refusing to sign a universal peace accord for no reason but superiority issues. However, the end of the book makes it clear that the scientist was only giving half the issue - the aliens are asking for some truly jawdropping accommodations for their "peace", and several other species are against it. The Lost Colony further reveals that the aliens behind the accords are real pricks, and that humanity (while pretty arrogant) isn't all that bad in the end. The overall balance of the series shows humanity as flawed, but not monstrous.
In Gullivers Travels, the final voyage has Gulliver land in a place where he encounters the Yahoos - mindless, crude beasts that are visually indistinguishable from humans. To the point that the "enlightened" (and horse-like) Houyhnhnms eventually forbid him from staying because he's too much like them. They try to use moral threat as a Freudian Excuse, but they're obviously not really afraid of Gulliver's baser moral tendencies. This moral contradiction makes the Houyhnhnms even bigger bastards than anybody, but Gulliver is so wrapped up in his newfound misanthropy that he doesn't notice (or probably doesn't want to).
Another fine candidate for the title of magnum opus of fictional Human Bastardry is an illustrated science fiction novel entitled Man After Man: An Anthropology of the Future. Twenty Minutes into the Future, the well-to-do people of the world set off to leave Earth and colonize other worlds. Before they do, they use genetic modification technology to physically alter the people who weren't able to afford the trip, changing them to survive in different biomes. Time passes and we get to see how the mutated humans gradually evolve over the eons after being left to their own devices - and then, suddenly, a race of Planet Looters invades Earth, enslaves the mutants, and strips the planet of its resources. For their next trick, they wipe out all life more complicated than bacteria. Those invading "aliens" were actually the unrecognizable descendants of the humans who'd left Earth millions of years ago. Dude...
This is all the more jarring considering that the author, natural historian Dougal Dixon, never before addressed this issue so anviliciously. His previous illustrated novels mostly avoided it by taking place in alternate timelines where there were no humans at all (there are hints of Gaia's Vengeance as the setup for After Man -look at the title- but that's as far as it goes).
Just to be clear, the genetic engineering wasn't forced on those left behind, and it was actually done in a belated guilt-trip attempt to replace the many, many species humans had already wiped out. And the ones who eliminated virtually all life at the end had long since forgotten their origins on Earth, let alone that they were distant relatives of the creatures they were destroying.
Often comes through in Tales Of MU, which focuses on the lives of non-human students at a university with Fantastic Racism. Not that the merfolk, ogres, (surface) elves, or kitsuyokai are any better.
Many of S.L. Viehl's s-f novels fall into this category. The vast majority of "Terrans" are rabid xenophobes: Extraterrestrial sentients are only allowed on Earth under very limited circumstances, certainly aren't allowed to live there, and will generally find it an unpleasant place. And if you're discovered to be a Half-Human Hybrid(or a clone)...heaven help you.
They will also send a fleet to sterilize your world if they find out you're harboring a human clone. Somehow, the humans seem even more monstrous than the Hskt-skt.
A constant theme running throughout H. G. Wells' The Island of Doctor Moreau. Reaches an early peak with the ship's crew that forces Prendick off the boat and leaves him to die in the middle of the ocean. Moreau's creations of demihumans he and Montgomery dominate isn't so sweet either.
Author Tad Williams seems to be fond of this trope with the Memory, Sorrow, and Thorn series and the Shadowmarch series. Faerie races exist in both: in the former it is the Sithi (immortal elves), while in the latter it is the Qar. In both instances, humans attempted to carry out a campaign of genocide against the kingdom of Faerie for no other reason except they wanted the land or they thought the Faeries were evil. In the Memory, Sorrow, and Thorn series, the Big Bad is a dead Sithi prince who gave his life defending his people against human invaders and now wants his revenge. Unfortunately, it seems he's willing to destroy the world to do it, so even the remnants of his people rally to fight him. His final undoing? The one human who actually bothers to apologize.
Robert Zubrin's The Holy Land. Earthlings and non-Earthlings disagree on who are the 'humans', but this trope applies to either and both of them regardless.
In the David Weber authored Bolo books there is direct neural interfacing between Bolo commanders and the later model Bolos (Battleship size self-aware tank). A Bolo has a warrior personality but nobody had realised how much the safeguards had inhibited its ferocity until they saw the first Bolo-Human mental fusion go into battle. Humans have no inhibitory safeguards.
It's worth expanding, the Bolos with the Human Mental fusion end up going on a generations long genocidal war against a larger alien empire. Thousands of worlds, Trillions of humans and aliens, and only a few million survive on a few very backward planets.
In The King of Beasts by Philip Jose Farmer, an alien scientist shows a visitor how he's cloning several now-extinct animals. At the end, he shows one he had to "get special permission to raise." The visitor is shocked, and begins to ask-and is confirmed-that it's a man. Then again, the scientist seems to pity the growing human, since it'll be "all alone."
In the Callahans Crosstime Saloon series, humans are bastards because of the Krundai. They are pacifistic carnivores, and hit upon the idea of breeding food that kills itself, so they shaped humanity into being the most savage, self-destructive species they could.
In The Acts of Caine, humans are bastards. Well, to be exact, the metaphorical psychomorphic deity-incarnation of humanity is a bastard. But the human hero who achieves its humiliating defeat is also a bastard, so in this series humanity doesn't look good at the individual or species level.
Subverted (the Qu), played straight (the Gravital) and everything in between in Nemo Ramjet's All Tomorrows.
In The Killing Star, by Charles Pellegrino and George Zebrowski, an alien species annihilates humanity with relativistic kinetic weapons before we even encounter them. They had been observing humans, and had discovered that our technology was nearing the point where we could build relativistic kinetic weapons ourselves, so they wiped us out on the off chance that we might decide to wipe them out. Why does this story qualify under the Humans Are The Real Monsters trope? Because the authors made it quite clear that we would have done exactly the same thing to them if our roles had been reversed.
This does qualify the aliens as bastards, though (if we're the same as them, they're obviously the same as us).
In Run to the Stars, by Michael Scott Rohan, we get the following exchange, after Kirsty and Ryly discover that the world government has sent a missile to wipe out a just-discovered alien species:
Kirsty: "There must be millions of inhabited worlds out there, whatever the experts spout. Some like us, some not. Sooner or later one of them's bound to track back our communications overspill and find us. What then? Under the bed? If that missile hits the target, we'll have tae hide. Shrink back into our own wee system, never make a noise, never stir outside it. What if any other race ever found out what we'd done? Then we'd never be safe. They'd never trust us. Not for an instant. There's bound to be some of them who think like you, Ryly. We'd be giving them grand evidence, wouldn't we? They'd wipe us out like plague germs and feel good about it!"
Ryly: "Unless... Unless we got them first. At once, on first contact. A pre-emptive strike, before they could possibly have a chance to find out about us. Hellfire, isn't that a glorious future history for us! A race of paranoid killers, skulking in our own backwater system when we might have had the stars! Clamping down on exploration, communications, anything that might lead someone else to us and make us stain our hands again with the same old crime... Carrying that weight down the generations. What would that make of us?"
Kirsty: "Predators. Carrion-eaters - no, worse, ghouls, vampires, killing just tae carry on our own worthless shadow-lives."
Alan Dean Foster moderates this in his trilogy The Damned. Humans appeared in a world where all life would be impossible by the standards of most aliens, and we went through some unpleasant evolutionary contortions to survive, but if we last much longer without outside interference, we'll achieve peace. Unfortunately, outside interference is coming — and by book 3, after a thousand years as Cannon Fodder in an interstellar war, the humans are less "human" psychologically than the aliens are.
In Stross's Saturn's Children, the humans can't create artificial intelligence on their own, so they build machine analogues to human brains, then raise them as children and teach them what they need to know to fulfill their eventual robotic function, then record and duplicate a snapshot once they've learned enough. But wait! That produces people, who might resent slavery, so on top of that they hardwire a version of Asimov's Laws, to make them good little obedient slaves. But wait! That still leaves the inner person able to figure out loopholes, and isn't nearly bastardly enough, so to ensure that they cringe away from any thoughts of rebelling, they resurrect good old-fashioned slave-breaking techniques, and make rape and abuse of the adolescent robots the next level of conditioning.
Done in a harshly anvilicious fashion in a Neil Gaiman short story, "Baby Cakes", where humanity suddenly realizes that it has made most of the various animal species extinct, and bemoans the fact that now we have nothing to perform medical tests on, no meat to eat, no source for products like leather and such. But, the text says, humanity is clever, and we figured a way out of that, by using the least productive members of society to replace all that: babies. The end of the story notes that now the babies seem to be gone, but humanity is clever. We'll figure a way out of this...
The Dark Ones in Night Watch take this as a basic tenet, though the Light Ones disagree. Case in point: the Light created Communism to try and improve humanity. They claim it was subverted by the Dark, but the Dark maintains they didn't do anything, and humans simply went on a destructive path as a result of their own natures.
Update: the experiment with Communism was indeed sabotaged, by none other than Gessar the Brightest, head of the Moscow Night Watch. He revealed later that he had foreseen that the experiment would've been successful and indeed propelled the technological level of humanity but eventually would've lead to a 1984-esque world division into three constantly warring blocks and, most importantly, exposure of the Others and their subsequent extermination. So yes, basically it's implied that even given a perfect world, we'd screw it up.
In Sergey Volnov's Army Of The Sun, humanity has conquered and enslaved any alien race they happened to come by, imposing their culture and customs on them (apparently, some aliens didn't look too kindly on the introduction on the concept of love to their emotionless mating practices). The novels describe the galaxy after the empire-wide rebellion, which resulted in an alien-dominated galaxy, where humans are treated as second-class citizens. Interestingly, the novels make the reader feel more for the humans, even though it is clearly stated that humans were anything but kind to their alien slaves. In fact, the only races that they treated more or less fairly were Human Aliens, as they happened to look almost exactly like blacks, whites, and Asians. Then again, the aliens don't exactly treat humans kindly either, still remembering the days of The Empire. On the other hand, hardly anyone ever mentions the positive aspects of the Earthstella Empire, such as technological uplifting, introduction of FTL travel (only one other race managed to develop it on their own), unified language, interstellar economy, and turning a bunch of isolated species into a galactic community.
Only one alien dockworker nostalgically remembers the days of The Empire, when the spacedock was bustling with ships and work was always available.
A rather nasty science fiction novel by Charles Pellegrino, Flying to Valhalla is built around the theory that a species looks out for itself only, destroying all competitors. This includes humans, which they go on to prove, whether they want to or not.
Lampshaded in S. M. Stirling's Draka series. The Draka admit that they're bastards, and frequently upbraid the Alliance for its hypocrisy in not owning up to the bastard deeds of their own history: "We couldn't exterminate our aborigines, the way the Yankees did."
Ursula K. Le Guin's novella The Word for World is Forest features humans descending upon the forested planet of Athshe, harvesting the valuable lumber and terrorizing and enslaving the native inhabitants.
Tarrou, of The Plague, holds the worldview that evil is inherent and natural in humans:
I know positively–-yes, Rieux, I can say I know the world inside out, as you may see-–that each of us has the plague within him; no one, no one on earth is free from it. And I know, too, that we must keep endless watch on ourselves lest in a careless moment we breathe in somebody’s face and fasten the infection on him. What’s natural is the microbe. All the rest-–health, integrity, purity (if you like)-–is a product of the human will, of a vigilance that must never falter. The good man, the man who infects hardly anyone, is the man who has the fewest lapses of attention.
In Honor Harrington the Planet of Sphinx is a subversion where humans come to a planet inhabited by Noble Savage creatures called treecats and instead of tearing the planet up, they go to lengths to keep it clear of development, and form friendships with them. One of them bonds with the title character who of course is an exponent of another trope about humans.
A rare occasion when this trope is played in positive (kind of) light occurs in a short sci-fi story "Cage" by B. Chandler. A group of astronauts are marooned on a distant planet and then captured by aliens. Humans are treated well but are not recognised as sentient beings. The obvious solutions, like making right triangles out of twigs, fail to impress the aliens. However, later humans discover some small vermin scurrying around their cage and decide to capture it and keep it as a pet. The succeed, and right afterwards the aliens let them go with apologies. What can better serve as an evidence of intelligence than an ability and readiness to put other beings in cages?
The galactic empire of Bill the Galactic Hero has a war-based economy that has to be sustained by seeking out new alien races with which to do battle. The aliens are treated well at first until the humans trump up some faux pas for the ambassadors to make which is made into an excuse for all-out interplanetary war.
They are currently engaged in a war with a race of Lizard Folk called Chingers, who are portrayed in the media as man-sized scary reptiles who will "marry your sister". In fact, Chingers are about 1-foot tall but incredibly strong thanks to them being born on a 10g homeworld. However, they were a race of pacifists until humans attacked them. Since then, they've learned to fight and spy pretty well, to the point where The Empire is losing the war.
HP Lovecraft played with this a bit. While not directly adressing the trope, he noted that among his gods there is one who is the most human of them all - Nyarlathotep. You know, the most malicious, manipulative and outright sadistic one.
He's also the only one who seems to actually notice humans and treat them as something even worth playing with. To the rest, if they notice humans at all, they aren't even worth the equivalent of burning with a magnifying glass.
Invoked several times in Animorphs, especially when Ax learns about things like the Holocaust - though very few of the aliens consider humans complete bastards, and most alien species are acknowledged to have a bit of bastard in them too (the Pemalites and the Hork-Bajir are the only races that are truly morally superior, and that's because they were genetically engineered to be kind and peaceful and to be stupid and docile, respectively). The Yeerks do have an attitude of "it's not like humans are so perfect anyway", along with the "you're our meat" thing, though.
In the Andalite Chronicles Elfangor is surprised to learn that humans fight wars with one another. However the Andalites are not much better given that they attempt to wipe out the human race in order to get the Yeerks twice.
British statesman Lord Chesterfield in Letters to His Son: "In the mass of mankind, I fear, there is too great a majority of fools and, knaves; who, singly from their number, must to a certain degree be respected, though they are by no means respectable. And a man who will show every knave or fool that he thinks him such, will engage in a most ruinous war, against numbers much superior to those that he and his allies can bring into the field. Abhor a knave, and pity a fool in your heart; but let neither of them, unnecessarily, see that you do so." (letter 60)
Averted in The Man Who Fell to Earth and its movie adaptation, because according to Thomas, his people would likely have treated a human visitor as badly as Earth's people treated him.
In the original version of I Am Legend, this is the ending twist. At the ending, Robert Neville finds the living vampires actually imprison him and sentence him to death, learning they are terrified of him; since Neville is the last human, and his idea of survival was murdering vampires indiscriminately, it's revealed Neville is being put to death because he's the true monster.
The dolls of The Dollmaker are weird and alien (and, okay, occasionally murderous), but they pale in comparison to a normal (if sociopathic) man.