Some pesky population happened to get in the way and got exterminated as a side effect. For storytelling reasons the operation may not be called genocide or otherwise be made to sound bad. There are three basic ways in which this can play:
Admit it proudly, and inflate the figures. It wasn't just necessary, it was right. The demographic/species you exterminated were Always Chaotic Evil, and anyway A Million Is a Statistic. You might want to put narrative focus on how much better off all non-bad/normal/good people are now that the bad/weird/evil people are no longer around to contaminate and/or prey upon them. The only sad thing about any of it is how many non-bad/normal/good people suffered and died exterminating them. There's room for fudging the figures, but only upward - to make your extermination-achievement look greater, and your losses greater and/or more tragic as well.
In Code Geass Princess Euphemia is accidentally Brainwashed into wanting to kill all Japanese people, and the Brittanian military follows her orders to slaughter them. While the genocide is eventually called off, the Brittanians seem to consider the Japanese "a dangerous, belligerent race" because they dared to fight back when faced with annihilation.
After Frieza single-handedly exterminated the Saiyan race in Dragon Ball Z, he came up with a fake story about their home planet being destroyed by meteors that even his henchmen who were there stuck with, probably to avoid Genocide Backfire from the few surviving Saiyans left. It didn't work, of course. He was none too secretive about his other genocides, however, which just went to show how afraid of the Saiyans he was.
In the Lucifer volume Mansions of the Silence, Lucifer annihilates billions of souls as a side effect of saving the life of one single person. (That one person was someone he owed a favor, his billions of victims were not.) Of all the people who witness this tragedy, only Bergelmir says anything about this action being immoral, and even he is quite polite about it. Even so, everyone else simply ignores him as they would a person who's being generally rude, impolite and socially inappropriate. Those present know that annoying Lucifer is really not the best course of action if your plans involve seeing another day, so they're probably staying quiet out of simple self-preservation. But in any case, elsewhere in the comic it is mentioned that it's impossible to destroy a soul - it simply unravels and then rewinds itself over millennia. And considering that the Mansions of Silence are in some ways worse than Hell, it could just as well be said that Lucifer granted their inhabitants a break from their usual torment.
In the Strontium Dog arc "The Final Solution", The New Church publicly claims that they're moving the mutant population in New Britain to new homes in another dimension where they can live in peace away from normal human beings. What they're really doing, however, is rounding up mutants from their ghettos and dumping them in a dimensional wasteland to be stranded and killed by an Eldritch Abomination, but they know that nobody would make much fuss if they make it sound like a peaceful relocation program. A particularly nice bit of calling-out, given that Magneto is, famously, a Holocaust survivor:
In Weaver Nine The PRT has a blanket kill order on every and all members of the Society. Given that very few of them have committed crimes worthy of a death sentence, and the fact quite a few of them are innocents who joined the Society in gratitude after the Society rescued them from slavery, unjust imprisonment, torture, or other terrible fates... it reeks of Genocide.
In addition: Weaver's Society is all but legally a nation unto itself, with infrastructure, territory and such. Most obvious in when she offers forty citizens to the defense of Brockton Bay, more than half the number of capes the Protectorate could gather.
The Conversion Bureau has ponykind forcing mankind to "convert" en masse into ponies. If they don't, they're killed. That this is genocide is ignored by both the ponies and the authors, who see it as the best possible thing that can be done. The fact that the authors gleefully ignore this and in fact treat it as a good thing (sometimes going so far as to vehemently defend it) is actually frightening. However, most deconstruction stories often subvert this trope where humans and ponies alike realize the true meaning behind the bureaus and often rebel against Celestia.
Lines And Webs non-equine races can't be magically mind controlled by Celestia to stop them from being violent, so she plans to drive their species to extinction in order to enact her vision of a peaceful harmonious world. Interestingly downplayed, Celestia doesn't want to actively commit genocide, just cause their civilizations to shrink until they die off naturally. Of course, its still resulting in mass starvation, so it really isn't any different.
Titan A.E. ends with the energy-based Drej being annihilated and recycled as fuel for a great world-building project. The film starts with the Drej themselves committing genocide against humans by destroying Earth. Only a few thousand humans are left, scattered among the stars and treated as scum. Bitterly ironic as well, as the Drej's prophecy wound up becoming self-fulfilling due to their paranoia. If the Drej hadn't chased the humans to Titan, then it would have been just a very large derelict within an asteroid field, as there wouldn't be nearly enough power to activate it.
The Evil Empire regime removes the galactic senate just before they destroy the populated planet Alderaan. Thus, there is no Senate that can protest against this atrocity. While they don't say outright that the upcoming demonstration of the Death Star's firepower is the reason why they removed the senate, it sure is convenient timing.
The Expanded Universe explains events a bit more. The Emperor wanted to disband the Senate for quite some time before the events of A New Hope. He used the outing of Princess Leia, a member of the Imperial Senate, as a Rebel agent as a pretext to finally disband it. It was one of the last symbols of the Old Republic (something he wanted to be rid of entirely) and potentially filled with Rebel sympathizers.
Never Let Me Go: People "are completed" on an industrial scale. And "completed" actually equals harvested for their organs. The main characters are clones who have been created specifically for this task.
Speaker: This cure is voluntary. Nobody's talking about extermination.
Magneto: No one ever talks about it; they just do it. And you go on with your lives, ignoring the signs all around you. And then one day, when the air is still and the night is fallen, they come for you.
Speaker:[interrupts] Excuse me-
Magneto: Only then do you realize that while you're talking about organizing and committees, the extermination has already begun.
Magneto is exploiting this trope, however: he is using fear of genocide to widen the divide between mutants and humans and perpetuate his war against humanity, ostensibly to protect the mutants from just such an extermination.
Played straight to the very end of the Critters quadrilogy. Even in the last movie, where they hint at this trope being in place, when the crites have almost completely been annihilated but cannot be completely made extinct because galactic law prevents doing this, those trying to protect the last of the critters assume the role of the 'bad' guys, even though one of them, the shapeshifter 'Ug', was a returning 'good guy' from all the previous movies. In the end, the 'bad guys' are defeated and the last of the crites are destroyed and that evil bastard Ug who was trying to save them from extinction is killed as well, and there is much rejoicing. Ug had the upper hand in the situation, but the 'good guys' took him down by pointing their guns at the last of the crite eggs, and he had to make a fatal mistake trying to protect them. Isn't it nice when the 'good guys' use sleazy bad guy tactics to kill the virtuous bad guy?
In the Holocaust drama Conspiracy, the words "extermination" are almost never used, and are not written down as such by the secretary. Instead, everything is couched in euphemisms. Interestingly this was before the specific word "genocide" to denote such mass slaughters was coined. Coupled with the Translation Convention, Kritzinger and Lange struggle to come up with something that would encapsulate it as "war" is thoroughly insufficient and settle on "chaos".
R. A. Salvatore's novels about Drizzt feature the massacre of entire groups as a social institution for the dark elves of Menzoberranzan, although usually conducted on a smaller scale then genocidal: Killing a group of people is a crime, but only members of that group can make the official complaint. Thus: If you successfully kill everyone, so no one is left to protest, no crime can be said to have been committed. Ironically, this institution is also a part of how they maintain social order: If one of the royal houses falls out of favor with their evil Goddess, then other houses will use this system to gang up on them.
The Illuminatus! Trilogy: In one of the many versions of the backstory, Gruad has just destroyed Atlantis, wiping out its entire population: "But deep inside, he knows that what he has done isn't nice".
The Andalite military's plan to "quarantine" planet Earth to keep the Yeerks from using the resources (especially the Human Resources) of Earth to conquer the galaxy. But it's not actually militarily possible to enforce this quarantine—so everyone treats this as an euphemism for genocide.
Ender’s Game. Throughout the book Child Soldiers are being trained to fight in case an alien race known as the Buggers invade like they'd done twice before, the last time being 70 years prior. It turns out in the end that the Child Soldiers were actually being trained to launch an invasion against the Buggers, resulting in the extermination of their species via Earth-Shattering Kaboom while tricking the children into thinking they were only playing a game. The Buggers themselves, thought to be Always Chaotic Evil by most Earthlings and portrayed as such in propaganda, were actually peaceful, having ended their hostilities against mankind generations ago. And the initial hostilities were an honest misunderstanding. They didn't mean to start a war, they were just saying "hello" by introducing their drone-soldiers to our territory and having them fight a bit. Drone-soldiers killing each other is roughly analogous to a hand-shake because each individual drone has no mind of its own. They had no idea that ALL of our drone-soldiers were actually individual Queens. How insane is that, an entire race of Queens and nothing but Queens? Who could possibly have predicted such a form of intelligent life existed? They became passive when they realized this, in the sense of only now fighting a defensive war. They made no further attacks and merely tried their best to not be wiped out by the vengeful hand of humans, who they were trying desperately to communicate their apology to. (It nearly worked.)
In the children's book The Inventors, the two main characters Nate and Cat have won a scholarship with the world's greatest inventor Ebenezer Saint, who they discover is planning to destroy humanity and start rebuilding society from scratch. At one point, Saint begins rolling out a list of euphemisms for what he's about to do, before asking for suggestions for more. He accepts Nate's suggestion of "Begin the genocide", but calls him a drama queen for it.
In Harry Harrison's Deathworld, their world has gotten really too deathy, so they decide to emigrate. There is a nice planet with a nice plateau BUT the plateau is inhabited. The Deathworlders suggest simply eliminating this population. 'Oh no' says the hero, 'that would be wrong'. Instead they lead this war-like race off the plateau to rich farmlands where they can cut a swath through the native population, enjoy their luxuries, get seduced by the lifestyle and never return to the plateau. This wholesale slaughter is 'oh well you can't make an omelet without breaking a few eggs'.
Likely the largest genocide ever imagined is at the conclusion of the Skylark of Space series. The protagonists have before tangled with the "ameboid" Chlorans, who attack, enslave and exploit humans (but do not exterminate them). In the earlier encounter there was just one Chloran planet; the option of genocide (called explicitly by that name) was considered, but due to pleadings of "soft-hearted" women the milder option of sending the planet far away was taken. But when discovering a faraway galaxy with millions of Chloran planets, the protagonist Seaton decides that the Chlorans are "a cancer" and a danger to the entire universe, and that nothing would do but to kill every single one of them - emphatically rejecting any other option. He and his arch-enemy turned ally DuQuesne proceed to do just that, causing all the Chloran suns to go nova. "The Chlorans died in their uncounted trillions. The greeny-yellow soup that served them for air boiled away. Their halogenous flesh was charred, baked and dessicated in the split-second of the passing of the front wave from each exploding double star, moments before their planets themselves started to seethe and boil. Many died unaware. Most died fighting. Most died in terrible, frantic effort to escape... But they all died." Immediately afterwards, DuQuesne - feeling not the slightest remorse at having just killed uncounted trillions of sentient beings and destroyed an entire galaxy, proposes to his long-cherished lady love and is thrilled to hear that she truly loves him.
In The Hunger Games when the revolution breaks out the population of District 2 do not join at first. They barricade themselves in a fortress called the Nut. Gale comes up with a plan to destroy it with an avalanche, and he also wants to bomb the exits to ensure nobody survives. The reasons he states for wanting to do this is that 'we'll never be able to trust them again'. While the rebels agree to leave the exits open, they still go through with the plan and hundreds if not thousands die as a direct result of Gale's actions.
If you consider allowing a race you could have effortlessly saved to die because of a non-interference policy to count as genocide, Captains Picard, Janeway, and Archer from Star Trek all committed genocide, in this case calling it principle (they justify it as not interfering with evolution).
In the Star Trek: Voyager episode "Living Witness", an alien civilization called the Kyrians remembers an encounter with Voyager centuries ago very differently from what really happened. Because Voyager traded with the Vaskans, one of their enemies, they revised the events to make Voyager a bunch of bloodthirsty villains who slaughtered their people. Evil Janeway doesn't share the Vaskan ambassador's concerns about annihilating the Kyrian population.
Janeway: Defeat... genocide... why quibble with semantics?
While people are getting slaughtered by the thousand in Equatorial Kundu on The West Wing, C.J. Cregg is not allowed by the White House legal counsel to say the word "genocide" in front of the press. This was in reference to the Clinton Administration standing by with the Rwandan Genocide going on, which they referred to as "genocide-type acts" because acknowledging it was genocide would mean under the Genocide Convention they were required to intervene. Unlike the fictional administration on The West Wing, they never did.
In The Event, when the only possible refuge left for the aliens is Earth and its resources clearly won't suffice for both them and the humans, Sophia concludes that "we need to make room". One of her henchmen, who had until recently acted as The Mole inside U.S. government and gradually grew to sympathize with the humans, immediately calls her out on it: "You mean GENOCIDE!"
When the human fleet of Battlestar Galactica discover a disease that could wipe out the entire Cylon race, Helo seems to be the only one willing to publicly describe using it as genocide. Adama does admit in private that he views it as genocide, however.
It eventually becomes clear that pretty much everyone realizes it is genocide, they just don't care.
Uther Pendragon in Merlin views his slaughter of magic users and all dragons except one as completely justified. His son, Arthur, goes along with it to please him, but it's repeatedly shown that he will not kill harmless magic users if he isn't forced into it.
In Black Adder The Second, Edmund briefly becomes Lord High Executioner, or as he calls it: "The Minister of Religious Genocide". It's his responsibility to execute "traitors" and closeted Catholics by command of Elizabeth the First. Notably the episode never moralises on genocide, and Edmund regards it as nothing but a tedious and very deadly chore he has to do.
In The Vampire Diaries, Elena causes the slaughter of tens of thousands of vampires without blinking, justifying it because it brings her closer to a cure.
In the Mass Effect series, the extermination of the vast majority of the Quarian race during the Morning War is successively downplayed from one title to the next, with dialogue in the first game stating directly that "the Geth killed billions and drove [them] from [their] homeworld," the second game limiting its description to "the Geth drove [them] from [their] homeworld," and the third presenting it as the conflict in which the Geth "won their freedom."
Although, worth pointing out that the Quarians (or at least their authorities) tried to do this to the Geth first. They didn't view it as genocide because as far as they were concerned, the Geth weren't actually even living, thinking beings. The Quarians didn't deserve to be almost wiped out, of course, but they weren't entirely innocent in the whole mess.
In StarCraft, Mengsk crosses a Moral Event Horizon by having the entire civilian population of the planet Tarsonis slaughtered by the alien Zerg so that he can crown himself emperor. In StarCraft II, he starts out as a Villain with Good Publicity who have managed to erase all traces of his crime. His loyal lackeys all shut up about it (or did he have them all assassinated?), and in the public social life of the empire it's out of line to point out that the Zerg invasion of Tarsonis was convenient for Mengsk's powergrab. To imply that the emperor was actually behind the attack is surely out of the question. Of course, there is one single exception to this dreadfully polite silence: Our hero, the main character, the "Traitor & Terrorist" Jim Raynor. Oh, and the genocide really backfires on Mengsk once the hero's forces have taken over the television network so the truth can no longer be suppressed.
Sonic the Hedgehog 2 had a planned-but-deleted zone called Genocide City, which was renamed to Cyber City, then replaced by the third act of Metropolis Zone after the Japanese developers bothered to look up what the word meant.
In Halo 2, after the changing of the guard, the remaining Prophets initiate an Order 66-style genocide of the Elites, disguised as a Brute uprising.
Yggdra Union has lots of genocide as "justice" when you get to the part where Yggdra has finally forced the Empire out of her country, then decides to invade Bronquia and destroy it. Even after Kylier tries to get her to realize that she's going to become the new 'evil invader', Yggdra tells her "This is Justice." Then the game forces you to mow through the 'Bronquian Militia', which is a basically a bunch of level 1 units trying to defend their homeland, and makes you feel very bad about it. "What is Justice?" is a question that a lot of people are asking throughout the game.
A gameplay mechanic in Age of Wonders. When you take over a town, you have the option to "migrate" the race currently inhabiting the town, replacing it with a race that's friendly to you. It's a very useful option - say you're a good-aligned race but just took over an undead town and want to replace it with another good-aligned race - but you're still basically committing mass deportation and resettlement...
The Black Dragons are a genocidal breed of dragons that have been corrupted by the Old Gods, and now serve their insane master on his quest to kill everything. In the face of this threat, the Red Dragons, after many years of conflict, decide the only thing to do is to declare every single Black Dragon corrupted and beyond redemption, and to exterminate every last one of them. That's every Black Dragon, Drake, Whelp, and Egg. And the player helps them do this, even personally dispatching the last fertile Black Dragon female and smashing her eggs. The irony of the Red Dragons, the Protectors of Life, being forced to declare indiscriminate oblivion on an entire species is not lost. However in a far distant and unrelated quest, there are signs that the Red Dragons have taken steps to purify a Black Dragon egg and to restart the flight anew. With one member: Wrathion who ended up killing off the entirety of the Black Dragon species, barring himself.
Also played straight with the war against the now homeless Zandalar Tribe and the remnants of troll species(barring the Darkspear who are playable).
The UN Convention on the Prevention and Punishment of Genocide compels all nations that have signed it to act with full force to stop and prevent any acts of genocide in the world. Most modern versions of this trope are usually countries trying to cop out of this agreement since they do not have the resources to/have the desire to get involved in a long, drawn-out conflict with little apparent gain to the intervening countries ("It's a civil war, not a genocide!"):
During the genocide in Rwanda and the slaughter of a large chunk of the population for being the Tutsi and not Hutu, the UN and major nations insisted on calling the events genocide-like acts as a way of loopholing out of doing anything. The USA was a particular abuser of this – since the Somalian intervention in 1993 blew up in their face, they didn't want to risk another failure. It got to the point that, shortly after leaving the presidency, Bill Clinton travelled to Rwanda to apologize for the horrible mishandling of the situation. Probably the best account of this is Michael Barnett's Eyewitness to a Genocide, which documents it from the perspective of someone who actually worked at the UN at the time (it isn't pretty).
During the genocide in Darfur, European authorities were very reluctant to call it a genocide, instead repeating the cop-out from Rwanda and calling it "Genocide-like acts". In this particular case, intervening would make them look bad, as intervention has become a very dirty word in light of the War on Terror. Thus it was not a genocide. This didn't prevent the International Criminal Court from issuing a warrant for the arrest of Sudanese President Omar al-Bashir specifically indicting him for three counts of genocide (as well as five counts of crimes against humanity and three counts of war crimes). The arrest warrant has not been served, as al-Bashir has made a point of not visiting any country that might arrest him.
During World War II, most Germans and a lot of people in the allied nations as well refused to acknowledge that the concentration camps were really death camps – even if they knew the truth for certain, it was so much easier to pretend it wasn't happening. To this day, there are still people who cling to the fantasy that the Holocaust didn't happen at all, or that it "only" happened to the Jews – thus retconning away the other victims: the Slavs, the gays, the intellectuals, the Romani, the mentally disabled, and so on.note Although the exact numbers will never be known, it's pretty likely that the majority of those killed by the Nazis weren't Jews, although Jews were still the single largest group killed by them (outside of combat anyway; far more Russians died during the war).
The Armenian Genocide, which was a Trope Codifier for 20th century genocides to come. The Republic of Turkey passionately denies it was a genocide to this day, mainly to protect their reputation and dodge having to pay reparations. There are citizens in Turkey who want the government to acknowledge the genocide, though they may not be the majority since the country is very nationalistic, and in fact people have been prosecuted saying genocide occurred under a law criminalizing "insulting Turkishness". This gets tied into international politics because Azerbaijan, an avowed enemy of Armenia and close ally of Turkey, demands that Turkey refuse to acknowledge the genocide. Not that Turkey's government is in a particular rush to do so anyway, Azerbaijan just gives them another excuse.
This particular one has repercussions elsewhere. A major controversy ensued when Abraham Foxman, head of the Anti-Defamation League, urged the U.S. Congress not to recognize the Armenian Genocide; unsurprisingly this was not considered becoming of one of America's most respected civil rights organizations. The internal conflict proved to be too much and the ADL has since downplayed the issue, though they're still against recognition.
This also extends to many of Turkey's allies. The US President for example must avoid using the "G" word when addressing Armenian-Americans on the Day of Remembrance for the genocide, using instead the Armenian term Medz Yeghern (The Great Calamity), which predates the creation of the word 'genocide' and has since gained Unfortunate Implications due to its use as a way to dance around having to say it was a genocide. For the record, although both George W. Bush and Barack Obama stated that if they became President they would issue a formal recognition of the genocide, Ronald Reagan is currently the last U.S. President to do so. 
Turkey's denial wouldn't quite be such a problem to Armenians if not for its constant foreign meddling whenever the subject comes up in other countries. Not only has it been successful in getting recognition of the genocide blocked in the US, but whenever the subject of making a movie about it comes up in Hollywood, Turkey finds some way to get the project shut down.
The situation is similar with what happened to the Pontic Greeks, considered a Genocide in Greece and of course not in Turkey. The Assyrians suffered a similar fate as well at around the same time.
Older Than Feudalism: The Roman destruction of Carthage and its entire population was widely lauded by Romans of its time as both just and necessary, with the worst aspects of Punic culture used as added justification for their annihilation. For years before it actually happened, Cato the Elder, a famous Senator, ended each speech he made with the demand "Carthago delenda est," Latin for "Carthage must be destroyed."
According to Azerbaijan's propaganda, Armenia is an evil nation at least in part because the Armenian army deliberately killed civilians during the Nagorno-Karabakh War.note Nagorno-Karabakh is a part of the Caucasus that is majority Armenian, but lies within the current borders of Azerbaijan (at one point, the distance between N-K and the Armenian border is only a few miles). Because of the linguistic and religious differences between Azeris and Armenians, and the fact that it had been a semi-autonomous oblast in the Soviet days, this became a problem very quickly after the Soviet Union collapsed. In particular, the Khojaly Massacre was the most infamous one, which was seen as completely uncalled for in the international community. The Armenian government continues to deny the massacres committed by the Armenian army on Azerbaijan's citizens. There were pogroms on both sides of the conflict too, such as the massacres of Armenians in Baku and Sumgait which Azerbaijan denies took place, though Khojaly was still worse in terms of casualties. So it's more like two countries doing this to each other. Hence the Azeris demand for Turkey not to recognize the Armenian genocide, in retaliation.
The disappearance of Muslims from Greece (and, later, the rest of the Balkans excluding Bosnia, Bulgaria, and Albania) is sometimes incorrectly identified as this. In 1923, after the long and bloody affair that was the Turkish War of Independence (in which the Turks soundly defeated the British, French, Italians, and Greeks put together), the Greeks and the Turks jointly negotiated a treaty providing for the exchange of populations: Greek Orthodox Christians in Turkey for Muslims in Greece. As a result, approximately 1.5 million (surviving; the Turks had already perpetrated the Pontic Greek genocide, which claimed between 750 and 900,000) Christians for about 500,000 (surviving; there had been reprisals, pogroms and other atrocities perpetrated against Turks and Jews in Greek Macedonia since the Ottomans had ceded it) Muslims. The incredible, full-circle irony of this is that the population transfers were based on religion, not ethnic or cultural identity. The result was that many Greek (and Greek-speaking) Muslims were deported to Turkey and Orthodox Turks were expelled to Greece. The whole affair remains a source of much bad blood between Greece and Turkey (though they've both grown closer recently), and many people from both countries feel they were more the victim, and it's one reason why the Armenian genocide is a Berserk Button issue in Turkey, being seen by many as a Double Standard. Still, as it stands today, Turkey is about 99.8% Muslim (some sources put the Christian population of the country at about 1,000), while there remain large Muslim populations in the Balkans (majority populations in Albania and Kosovo, minority in Bulgaria, and plurality in Bosnia).
The systematic extermination and/or relocation of indigenous people in the United States was generally depicted by contemporary writers and newspapers as justifiable, necessary, and inevitable, with few exceptions, and they were mythologized as a Dying Race to more or less cover up the fact that it was largely being done on purpose. This kind of myth was also used in Argentina and Australia, countries were European settler-immigrants also wanted the locals to make space for them (but not New Zealand or South Africa, where it was pretty clear that the locals were there to stay). Also used in The Raj (of 1848-1947), wherein the British consistently favoured static/agricultural nations and peoples over nomadic tribes - most famously in Burma, where they managed to piss off the mountain tribes enough that they sided withthe Japanese.
For some Jews, it's a case of "Would be rude to say 'Holocaust'". Jews often see their mass destruction as something unique in scale (mostly justified, as genocides of this scales have arguably never took place: some might say the Holodomor claimed more victims, depending on the assessed figures you look at), which makes any other massacre a level below it (or several levels below it). Abraham Foxman, head of the Anti-Defamation League, was filmed meeting with the President of Ukraine, telling him to stop referring to the Holodomor as a ‘Holocaust’. Ironically (or perhaps not), the Palestinian name for their loss and expulsion in the first Arab-Israeli war means "The Catastrophe" as well.
There is in fact a school of thought within Jewish studies, endorsed by scholar Steven T Katz and apparently believed by the Anti-Defamation League, that the Holocaust is not only unique but also the only true genocide to have occurred ever. Katz also holds that Gypsies and other non-Jews who also died during the Holocaust don't count as genocide. Critics (most genocide scholars, including Jewish ones) see this line of thought as just about as bad as genocide denial done by a perpetrator.
Whether the Manifest Destiny period of the US counted as one towards the Native-Americans varies hugely on who you ask, with generational gaps accounting for a large portion of it. Aside from the numerous broken treaties with tribes, there were also boarding schools whose primary purpose was to "properly" educate native children, barring them from speaking their native tongue and otherwise insuring they would be assimilated into the European-dominant culture in the US.
Peru has a similar story with Alberto Fujimori's "ligation days", but it's not Peru that denies it. Like Iran and a few of Israel's other neighbors with the Holocaust, this one involves countries unrelated to the actual perpetrator: The United States (mostly because of some American companies who supported Fujimori) and Japan (because Fujimori currently resides there).
In East and South-East Asia the Japanese are considered notoriously cavalier about their Army's war crimes during the 1930sand 40s. Part of this comes from genuine ignorance, as Japan's right-wing has been partially successful in preventing this from being covered in schools and school textbooks; they fear that acknowledging the 6-20 million deadnote Largely, boringly enough, from starvation-related diseases as per the Gulf of Tonkin Famine (c.2-3 million) in northern Vietnam, Henan Famine of 1942 in Guomindang China (another c.2-3 million), Indian Famine of 1942-43 (another c.2 million) in Bengal and other bits of The Raj that relied on Burmese rice imports, and a few other million resulting from tens of millions of people fleeing Japanese Occupation to live in the most impoverished and agriculturally-poor bits of China during the eight-year war, as well as the specifics of the various war crimes and crimes against humanity (biological weapons testing on hundreds of thousands, human medical experimentation on tens of thousands, mass-rape of hundreds of thousands, torture of hundreds of thousands, forced prostitution of tens of thousands, POW deaths from preventable causesnote starvation-related disease being the big one, of course and heavy-handednessnote like being bayoneted or beaten to death for failing to work hard enough because of disease and starvation in the hundreds of thousands, POW-beheading contests, etcetc) would harm the patriotism and national pride of Japan's youth. Interestingly enough, some surveys of national pride would appear to indicate that the advent of the internet has resulted in a dramatic decrease in Japanese patriotism.
Matthew White, a self-described "atrocitologist", has taken it upon himself to be a scholar of the absolute nadirs of evil human beings have committed. He coined the term hemoclysm ("blood flood") to describe the worst atrocities of history. While World War II tops the list in raw numbers with an estimated 55M deaths, when the ranks are adjusted for the world's population at the time, it drops to ninth. The Mongol conquests killed 40M in the 13th century (#3 in raw numbers, #2 in adjusted rank), and the An Lushan Revolt in the 8th century claimed 36M (#4 in raw numbers, #1 adjusted). None call these "genocides". Stephen Pinker, who used Matthew White's work as a tiny fraction of his research for The Better Angels of Our Nature, points out just how frequent the hemoclysms and genocides of history have been, and worse, how ordinary they were in the minds of the people of that era. Even more troubling is that despite the much lower world population at the time and lack of industry, numbers close to that done in the entire Second World War were achieved by pre-industrial societies.
Of course, this also conflates various types of killing; while the Mongols undoubtedly committed genocide a few times, a great deal of the death was not genocidal in nature. Also, the idea that it was "normal" at the time is modern-day revisionism and propaganda; it wasn't at all. Indeed, one of the major reasons that the Mongols were so harsh to some of their enemies was precisely to terrorize everyone else into surrendering, so that they didn't HAVE to fight as much. If their enemies just gave up, it was much easier for the Mongols to rule over them. Additionally, some of it was done to end endless intertribal violence; by simply killing all the older men (gendercide), they effectively deprived the losing tribe of the ability to take revenge. People like Vlad the Impaler and the Mongols are remembered precisely because they were unusually harsh, and they were well aware of the psychological impact on the enemy and took full advantage of it.
In addition, the numbers are deeply dubious and subject to dispute, with the supposed topper (the An Lushan Revolt) being case in point. Chinese sources on numbers and logistics tend to be somewhat wonky at the best of times especially regarding warfare. On top of this, a lot of the things used to gauge the losses of the An Lushan revolt are wonky, like using census and tax returns listing numbers of household (which don't just reflect the population loss but also the breakdown of the ability to count the people still alive).
Countless tribes were exterminated in tribal fighting, their names never recorded and the crimes lost to history.
The standard outcome of a defeated city was to be subject to massacre for much of history. For example, the 1258 Siege of Baghdad ended with roughly two million exterminated. This would be called genocide by most modern scholars.
The Bible chronicles the extermination of many peoples, in some case directly commanded by God. In one of the more famous examples, Numbers 31 states all male Midianites were killed by Israel, down to newborn infants, as were all women who were not virgins. The virgins were taken as slaves. The tone of the book does not indicate that this act should be condemned as genocide. The theological implications are not a good topic for discussion, but the tone does hint at how societies of the era viewed such horrors.
Paul Mojzes in his book Balkan Genocides argues that the Balkan Wars of 1912-13 were actually a series of genocides - ones that the world has mostly forgotten, partially because they happened in a rather remote area, and partially because the term "Genocide" had not yet been coined back then. He also argues that some of the events called "ethnic cleansing" (such as the war in Bosnia 1992-95) or "repatriation" (the expulsion of the Germans after World War 2) actually constituted genocide.
From 1976-1983 the National Reorganization Process in Argentina carried out an extensive campaign of what could best be called "politicide", exterminating 30 000 members of various leftist political groups. Right-wing supporters of the junta went into denial, with Ronald Reagan, Margaret Thatcher, and various other Cold War leaders all trying to paint the situaton as a civil war—at least up until the Argentines attacked British territory during The Falklands War.
Following the rift between Israel and Turkey due to the Mavi Marmara incident, an argument arose in the Knesset, the Israeli parliament, regarding the question of acknowledging the Armenian Genocide as such, mostly due to political reasons.
What the Belgians did to the Congolese is still up for debate as to whether it actually was a genocide; mostly because the Belgians did not try to exterminate the Congolese. However, if it does count as a genocide, then it would have caused far more casualties than the Holocaust. It does not help that Belgium has made Holocaust denial illegal, but denying this doesn't look like a problem; they still have a Monument of Leopold II where it is written "I have undertaken the work in Congo in the interest of civilisation and for the good of Belgium."