The Doctor: Do I have the right? Simply touch one wire against the other, and that's it. The Daleks cease to exist. Hundreds of millions of people, thousands of generations can live without fear... in peace, and never even know the word "Dalek".
Sarah Jane: Then why wait? If it was a disease or some sort of bacteria you were destroying, you wouldn't hesitate!
Towards the end of Darker than Black, the main character is faced with a choice, either let his enemies initiate a plan that would wipe out every contractor in existence, or stop them at the cost of wiping Japan (and presumably all it's inhabitants) off the map, literally. He doesn't want either to happen, but saving one would mean genocide for the other. He Takes a Third Option.
Secret Invasion: A What if... one-shot made a variant: the shape-shifting aliens Skrulls successfully invaded earth. They rule countries, live among humans, and even allowed humans to become skrulls. The Avengers, now a terrorist outlaw band, got a sample of the Legacy Virus adapted against the Skrulls. They face the dilemma: waste precious time trying to turn it into a vaccine, reverting the change in humans and removing the shape-shifting powers from the skrulls, or simply use the virus as it is and kill them all. in the end, it is the villain Norman Osbourne who uses the virus and causes the skrull genocide. He is beheaded by Captain America for it.
MLP fanfics about a war with the Changelings seem to gloss over this trope. If the Changelings are Always Chaotic Evil, then exterminating them is the only option for victory, with little objections from the heroes.
In the Alien franchise, somebody always seems to want to capture a live xenomorph....
But only to try to make them into a weapon. Lampshaded in the Green Lantern / Alien crossover, Hal points out that the xenomorphs are just animals, so they move the hive to Lantern Mogo (a living planet) since he can watch them and make sure no one runs into one.
For understandable reasons, Ripley in Aliens seems to have no moral reservations on this point:
Ripley: "Just tell me one thing, Burke. You're going out there to destroy them, right? Not to study. Not to bring back. But to wipe them out." Burke: "That's the plan. You have my word on it." Ripley: "All right, I'm in."
The great irony with the Xenomorphs is that they need live hosts in order to spread. One person = one Xenomorph. If people would just leave them alone they wouldn't be a threat.
The third film establishes that they can implant other mammals.
Keith Laumer's novel The Glory Game. After the warlike alien Hukk are defeated, the Terran Hardliners want to wipe them out to keep them from threatening Earth again.
Ender's Game and its sequels apply this in one way or another to every nonhuman species in the setting. None of them intended to start hostilities with humanity, and in only one case (when fighting a seemingly sentient virus that wipes out almost every life form it infects) is genocide portrayed as justified. With each species encountered, humanity is more reluctant to kill fellow rational beings, and the final species in Children of the Mind is dealt with in a completely nonviolent manner.
The Taxxons in Animorphs are driven by unceasing hunger, to the point that if one of them is injured, the others will eat its entrails. They voluntarily joined up with the resident mind-controlling parasites in the (unsuccessful) hopes that this would keep them from killing everything in sight. The issue of whether they need to die is ultimately sidestepped through a species-wide Metamorphosis.
A variant: the Hork-Bajir are a peaceful species, but to weaken them as a tool for the Yeerks Alloran decided to genocide them with a Quantum Virus, earning a What the Hell, Hero? from his own species.
Even the Yeerks themselves are the targets of this. At one point, an Andalite black-ops team visits Earth hoping to infect the enemy with a similar quantum virus to the one that devastating the Hork-bajir. Both the Andalite researches and the Animorphs are appalled (and in the latter case very worried) about the near-certainty of the virus mutating to attack humans; none of them seem to consider whether the Yeerks really deserve it. (Possibly because, with the exception of Cassie and sometimes Tobias, they agree — Jake never gets a chance at the whole species, but in the penultimate novel he deems some deaths necessary, to the tune of 17,000 unhosted Yeerks.)
Regardless of Vergere's motives, the Advisory Council is still split on what they should do with it: Luke Skywalker is repulsed by the idea of slaughtering so many innocents; Releqy A'kla thinks it would set a horrifying precedent that genocide is acceptable in war; Triebakk is worried the virus might mutate and kill the New Republic, too; and Ta'lam Ranth is worried the Vong might well genocide them right back if provoked. On the other hand, Cal Omas is keenly aware that they're losing troops and momentum, Sien Sovv has no confidence in his own ability to prosecute the war, and Dif Scaur... well, he commissioned Alpha Red in the first place, so you can guess how his vote goes. One of the reasons for the climactic battle of Destiny's Way is to regain some lost ground — any lost ground, to prove that a conventional war is actually winnable.
Except by this period of time the Sith are no longer a species, they're a cult/society. Ben isn't advocating the annihilation of every being amongst the Lost Tribe, though obviously many will die in the war that ensues, he's advocating the destruction of a culture built on a genuinely evil philosophy. In a similar way, the Allies of World War II spoke of destroying Nazism, not the German people.
This wouldn't have even been the first time it happened. After the Great Hyperspace War the Republic and the Jedi attempted to completely exterminate the Sith, who at the time were a species, mostly. It didn't take the first time but sources later in the timeline were mostly made before the retcon and maintain that the species is gone so...
L. E. Modesitt Jr. is rather fond of ending his books with this, and the heroes usually end up deciding to Shoot the Dog.
EE Doc Smith's Skylark Series ended with Skylark DuQuesne, where Seaton was debating whether he should or even could wipe out the Chlorans. Eventually after much angst he decided to do it, but during the battle he was incapacitated, and DuQuesne (who was the main villain through the series, and who had always sworn to kill Seaton if he had the chance) had to take over to finish the job on the Chlorans. He did so without a qualm, and "The man who slew a galaxy looked no different after the deed than he had before".
Stewart Cowley's Terran Trade Authority universe features the Laguna Wars - a nasty fight between Earth and mutinous humans who wiped out an alien civilisation centuries before and took over its machines. The adventure is written for children under ten but pulls no punches, especially near the end; when it's discovered that the cargoes the Earth forces were blockading (and which led the Lagunans to mount an ultimately unsuccessful last-ditch attack on Earth) were an antitoxin against a fungal disease in Laguna Nine's atmosphere. The occupation forces arrive to find to their horror that the entire planet has been completely depopulated. It's not total genocide - the industrial centre on Laguna Seven is still intact - but it's bad enough, and all the more horrifying for it being unintentional.
Subverted in Mike Resnick's book Birthright: The Book of Man. The other 13,042 sentient races in the Galaxy seem to have no moral qualms whatsoever about hunting Humanity to extinction. It's averted only by the fact that Humanity's last survivors - One man and three women - decide to go out with a bang (literally - they commit suicide by blowing up the planet they're on) rather than surrender and be executed. Same result though, I guess.
Averted in the Destroyermen series. It's been pretty clear from the get-go that the only way the Lemurians and humans will ever be safe from the Grik is if the Grik no longer exist. This means wiping them out, and wiping them out fast, since they spawn like mad and grow to adulthood in about five years.
Though this is subverted in Firestorm with the discovery of an offshoot species called the Tagranesi who later prove to be valuable allies.
In Wen Spencer's Wolf Who Rules, humans try to argue against exterminating the oni; Windwolf states flatly they will do it, because the oni breed like rabbits and have a total Lack of Empathy. He is not happy when they find a half-human/half-oni child — he had hoped for only adults — but fortunately, she demonstrates empathy, and the genocide can be limited to the fully oni.
In Living Alone by Stella Benson, the English witch tries to argue this with the German one.
"As one Crusader to another," she said, "do you find it does much good in the war against Evil to drop bombs on people in their homes? After all, every baby is good in bed, and even soldiers when on leave are anti-militarist."
"It always does good to exterminate vermin in their lair," said the German, trying restlessly to raise herself more to the level of her lighter companion, who was still perched on the surface of the cloud. "It is at home that Evil is originated, it is at home that English women conceive and bear a new generation of enemies of the Right, it is at home that English children are bred up in their marauding ways. It is on the home, the vital place of Evil, that the scourge should fall."
"Oh, but surely not," said our witch eagerly. "It is at home that people are kindly and think what they will have for supper, and bathe their babies. Men come home when they are hurt or hungry, and women when they are lonely or tired. Nobody is taught anything stupid or international at home. You can bring death to a home, but never a righteous scourge. Nobody feels scourged or instructed by a bomb in their parlour, they just feel dead, and dead without a reason."
In Sarah A Hoyt's Draw One In The Dark, when they are dealing with the grubs that two breeding shape-shifters with insect forms left behind, Tom is keenly aware that they are the offspring of two shifters who were most of the time human.
Battlestar Galactica: humans from a Cylon point of view. At the end of the Miniseries, the Cylons agree that they unfortunately can't give up pursuit of the human fleet even though it's left the Colonial solar system behind and just wants to get as far away as possible, because any survivors will inevitably return and seek revenge.
A more straight example: In the episode "Torn", the Colonial fleet discovers a virus that kills Cylons horribly and doesn't affect humans. Cue big debate about the ethics of intentionally infecting the Cylon Resurrection Ship with it. Despite the inevitability that the Cylons would have found a cure/treatment/ray gun that addressed the disease before being wiped out entirely (given their technological levels), the debate almost immediately leads to a member of the crew taking matters into their own hands to save the Cylons from the minor inconvenience of losing one resurrection ship (read: perceived genocide).
The page quote from Doctor Who, where the Doctor doesn't want to wipe out the Daleks for fear of being no better than they are. Since time travel's involved, it overlaps with Hitler's Time Travel Exemption Act - could you kill a child in their cradle if you knew they'd grow up to be a war criminal?
Over the course of the revival, as details of the Time War come to light, we learn that the Doctor was faced with a similar decision and he went through with it, wiping out the entire Dalek race and all the Time Lords in order to bring an end to the war as well as save all of existence from his corrupted and omnicidal race. Coping with what he had to do is a big part of his character arc over the first four and a half series.
And the Doctor even had to go through with it again in the Christmas Special The Runaway Bride. It was a split second decision and he gave the villain of the week a chance to drop the Villain Ball...but in the end the Doctor decides to drown the last offspring of an extinct species to save the Earth.
And then the Doctor exiles his half-human clone to a parallel universe for going through with Dalek genocide at the end of Journey's End, in order to save everyone and everything else in the universe.
In an alternate history, O'Neill had never met Teal'c, and as a result, Stargate Command attacked his homeworld for this reason.
Subverted in Season Five, again with O'Neill. Subverted in that he only threatened it, and that he most likely didn't consider the sentient computer virus that had taken over his Second in Command to actually be 'people.'
Star Trek. Klingons in The Undiscovered Country were a unique situation. An environmental disaster caused critical damage to their homeworld, which would almost certainly kill billions over the next several decades and probably plunge the Empire into a civil war. All The Federation had to do was sit back and "Let them die," as Kirk said. Instead the two governments decide to talk peace and mutual disarmament.
In Star Trek: Deep Space Nine, Section 31, an underground group in Starfleet, infects Changelings, leaders of the Dominion, with a virus that kills them - and because of their lifestyle, all Changelings are affected. The Federation discovers the cure, but refuses to hand it to the Dominion until Odo can convince the Dominion to surrender in exchange for it.
The Dominion itself, when presented with this situation 200 years ago (with the Teplans), decided to Take A Third Option: they infected everyone on a planet with a disease that doesn't kill everybody at once, but rather is hereditary, incurable and can kill the host at any random time. 200 years later, the Teplans still haven't even attempted to rebuild their society.
The third season of Star Trek: Enterprise, with the Xindi being convinced by an alien race that humanity would destroy them in the future, so they tried to avert this by creating a xenocidal weapon. Although the debates tended to center around whether the accusation was true (it's not), and although the inventor of the weapon has his doubts on the morality, averting their own genocide is all the justification the Xindi need to Kill All Humans. An alternate timeline shows them tracking down human colonies even after Earth has been destroyed. Eventually, the Xindi factions are divided on whether to go through with the plan and the majority of them join forces with the humans to stop the weapon from being used, including the weapon's inventor who dies in the process.
Star Trek: The Next Generation: Picard is faced with the option to implant an impossible problem into the Borg's consciousness through a recovered drone. This would cause the entire collective to spiral out of control trying to solve it, and ending them. However, the drone, named Hugh, has developed a sense of identity. Picard ultimately decides to release Hugh back, hoping the spark of individuality will spread through out the Borg.
Picard's choice pays off for a few hundred of them, but then Data's Evil Twin Lore takes command of them, as seen in the "Descent" two-parter.
In another Next Generation episode, the crew of the Enterprise meet a Sufficiently Advanced Alien who faced this dilemma. He was normally an Actual Pacifist, but when a warlike species attacked the world he was living on, killing people he cared about, he went into a fit of vengeful rage — and simply erased all members of that species from existence. He seemed to be genuinely struggling with guilt over his act. Captain Picard said that the Federation had neither the power nor the authority to judge the alien for a crime of such magnitude, and the Enterprise continued on its way.
Star Trek: Voyager began with this very dilemma, albeit in an indirect manner. Voyager was transporter to the other side of the galaxy by the Caretaker, a being with astonishing technology, who protects the Ocampa from the Always Chaotic Evil Kazons. The Caretaker died, and captain Janeway had a dilemma: use the Caretaker's array to return home, letting the Kazons seize it afterwards and destroy the Ocampa, or destroy it and try to get home some other way? Of course, she choosed the second option (if not, it would have been a film rather than a series). Sure, they wouldn't kill the Ocampas themselves, but they would feel responsible if the Kazon were capable to do that because of Voyager's inaction.
Magic: The Gathering's Phyrexians have this to some extent. While there are a few good ones, and the entire red Phyrexian faction of the last block is the Token Good Teammate of them (because asking a Vulshok or a goblin if he wants to take part in the Great Work is likely to result in missing a few parts), as long as a drop of Phyrexian oil exists, the Great Work can begin anew.
Task Force Games' Starfire. The fanatically racist and warlike Rigelian Protectorate was completely wiped out at the end of the Third Interstellar War under the Alliance's "Genocide Decree". The Alliance believed that all Rigelians everywhere had been slain until two planets were found with Rigelian survivors at a low tech level, leading to a quandary about what to do about them.
In the Homeworld backstory, the player race (Kushans AKA Hiigarans) were an aggressive, expansionistic race that the Taiidans battled and had nearly extinguished. The galactic outcry for mercy was such that they allowed the Kushan to leave and settle on a planet in the galactic rim after swearing to never use/develop FTL drives. Thousands of years later, the Kushan history is forgotten and their descendants discover the remnants of their original ship. To escape their dying planet, they set about repairing its FTL drive...
Also, the Taiidan are treated this way at the end of the first game, and are allowed to live mostly unmolested (save for having their very evil emperor killed).
In fact, the Hiigarans were so bad that the Bentusi had to interfere in order to stop them from wiping out the Taiidani. The reason the Taiidani kicked out the Hiigarans from the homeworld in the first place was because the Hiigarans have turned the Taiidan homeworld into an unlivable hellhole with orbital bombardment. Furthermore, had the Hiigarans peacefully given up their hyperdrive core instead of attacking the Bentusi, they still would've had a fleet to defend against the vengeful Taiidani.
In the sequel to In Famous you spend the game getting enough power to use the RFI to stop The Beast, but it turns out the RFI kills Conduits and anyone with the Conduit gene instead of just depowering Conduits. And to top it all off, the plague from the first game has grown out of hand and the only way to stop it is to activate the RFI saving humanity, but killing every Conduit, including Cole, or awaken the powers of every Conduit in the world, making them immune to the plague, but killing everyone else in the process. The final choice of the game revolves around choosing between those two choices.
Played beautifully straight with the Helghast in Killzone 2 and 3. They're so angry at the rest of humanity (and quite rightly so) that in 2 their Autarch, Scolar Visari, upon being arrested, predicted that they'd "choke the streets with [their] dead before [they] surrender", and the conflict would escalate until he'd be returned to power and begged to restore order. He then gets shot by an angry Marine.
In Killzone 3, it's proven that he was completely right: the war gets so bad that the ISA is forced to surrender to the Helghast. In the end, it took cleansing Helghan of life completely to stop them.
In Mass Effect, the Rachni are a sentient, if extremely alien, species of insectoids who were thought to be actually extinct; you have the choice of either setting the last surviving Queen free to let them repopulate, or wiping them out entirely. A harder choice than it may seem, since the Rachni went near-extinct due to them embarking on a war with the Citadel Races, causing significant loss of life, though the Queen promises to leave the other races alone.
In keeping with the trope, you'll have some characters arguing that you can't justify destroying an entire species no matter how how much damage it once caused (keeping in mind that the Rachni Wars happened almost 2,000 years ago), and others who argue that it's time to "finish the job".
In fact, the Queen's testimony implies the Rachni are a naturally peaceful species who only went to war because of Reaper indoctrination; if you rescue her again in 3, her Rachni will aid you in the war effort against the Reapers. However, if you don't save her in the first game, her Reaper-created replacement will betray you if you choose to save her.
Another example from Mass Effect 1, but somewhat inverted: you find out the bad guy has found a way to clone krogans freed from the effects of the genophage, the genetic disease that renders most krogans sterile. You have to decide to destroy the army, otherwise he'll have an unstoppable force. Needless to say, your krogan teammate is pissed. You can argue that Saren's cure only comes with being his slaves...or kill him.
In Mass Effect 3, at the end of the Rannoch arc, you get a choice between allowing Legion to upload Reaper code to the geth, rendering them sentient and intelligent (but dooming the quarians in the process), or killing Legion and allowing the quarians to tear the geth apart. Unless you jumped through enough hoops to Take A Third Option...
In Mass Effect 3, the "Destroy the Reapers" ending will also destroy every other artificial intelligence in the galaxy, including the Geth (if they are still alive) and EDI. Even worse, it's also the only ending that Shepard has a chance of surviving.
In Mass Effect 2, during Legion's loyalty mission, you have to choose between destroying the heretic geth once and for all or committing Heel Face Brainwashing on them. Legion leaves this decision to Shepard because he can't decide.
In Star Control 2 the Ur-Quan have one of these. After being enslaved for thousands of years by malevolent aliens and having to spend decades wired to artificial pain devices to defeat said aliens, they decide that the hat of Always Chaotic Evil fits all other species enough to warrant galactic conquest. They split over whether it's better to lock them up or kill them just to be sure.
They not only split, they actually start a millennia-long war over it. The victor will decide the eventual fate of the galaxy.
A major plot point in the WarCraft 'verse. After the end of the second war, the leaders of the Alliance were split on what to do with the (at the time Always Chaotic Evil) surviving Orcs. Stormwind, Dalaran and Lordaeron felt they should be spared, while Stromgarde and Gilneas wanted to execute them. Eventually, the decision to put the Orcs into labour camps in hopes that they could eventually be reeducated into proper members of society was made. This decision led to the latter two nations leaving the Alliance, though Gilneas would eventually rejoin during the fourth war.
Not just once. The orcs are tricked by Kil'jaeden into killing the majority of the Draenei. Several of them are clearly torn, as they know some of the Draenei personally and have a hard time believing them to be the monsters Kil'jaeden claims they are.
During the Cataclysm expansion, we finally hear Queen Alextrasza of the Red Flight (more or less unofficial leader of all the non-evil dragons) declaring that the Black Dragonflight is beyond redemption and must all be exterminated. Given that Black dragons have been Always Chaotic Evilevery time they've appeared for the last three or four games, this might seem like a 'no duh' choice on the part of the player. But consider how agonizing it must be for the Aspect of Life to have to make that decision.
The Protagonist faces this again when a certain demon demands that he kill Jack's Crew for their crimes. The hero can either agree to kill them (even though they're already brain dead), let Zelenin kill all the demons with the Hymn, or just kill the one demon making the offer.
In the backstory of Mark Rosenfeldter's Constructed World of Almea, after the humans finally defeat The Empire of the Always Chaotic Evil ktuvoks, the kings of the two human countries who brought them down discuss among themselves whether or not they should just march into the swamps and kill every last ktuvok, so that they could never enslave and brainwash humans again. They ultimately decide against it, because "they did not have the stomach for it." Of course, this turns out to be a bad idea, because the ktuvoks rise again.
In the Bionicle serial Reign of Shadows, Toa Helryx is trapped inside the brain of the Great Spirit robot, said robot houses the Matoran Universe, and is currently possessed by the mind of Makuta. If she does nothing, Makuta will be free to conquer the entire universe, but if she tries to destroy the nearby machinery, every being inside the Matoran Universe will perish as a result of the Great Spirit crashing down. She eventually decides to do it... but other characters stop her, which provokes a furious battle.
Subverted by Eridan in Homestuck; he hates the terrestrial portion of the Alternian troll population, and claims that he would happily eradicate the lot of them, even commissioning a (land-dwelling) friend of his to build doomsday devices (that unaccountably fail to work). But by the start of the comic, the other trolls have figured that his aquatic-supremacist rantings are all just a cry for attention, and that if Eridan were given a genuine opportunity for genocide, he would pass it up. Double-subverted when, in the end, Eridan really does flip the hell out, kills several of his fellow trolls, and destroys the Matriorb, the last hope of his species to repopulate.
The Order of the Stick. After a dragon threatens his family, Vaarsuvius kills the dragon, then briefly revives it so V can cast "Familicide", which kills the dragon's entire, very extended family. Since the entire dragon species only has about 4 family trees, and proliferate very slowly, this may well have doomed the species to extinction. V casting this spell is treated like a major case of Jumping Off the Slippery Slope, regardless of the fact that black dragons are Always Chaotic Evil. And now, V has had to wake up to the fact that the concequences were more rather varied and longer-ranged than s/he thought. Much more varied. Welcome to the dilemma in the trope title, V.