The Super-Paleolithic People (Choukodaijomonjin) from Gekiganger 3.
The Dark Kingdom and Dead Moon Kingdom from Sailor Moon
At the smallest end of the scale, Rozen from Rozen Maiden. He created a race of thinking, sentient creatures, made them blindly loyal, and commanded them to fight to the death until only one survives. Why? To earn his love. Only centuries later, after a pretender triggers a fake Alice Game, does he deign to show his face again ... to restore the status quo and reset the game back to start. With a grudging admission that "there are other ways to win besides battle. On the other hand, can a force, however mysterious, who creates a "race" with less than ten members really be considered a Precursor?
The Mu of RahXephon, a race of literally blue-blooded humans who vanished off the Earth several ten thousands of years ago due to one of their own experiments failing (the reason for said experiment? The scientist just wanted to see if it would actually work). The story happens when they try to come back, and the end of the series makes it very clear that they could effortlessly wipe out humanity if they really wanted. They don't, they only suppress the TERRA organization that is directly opposing them. Their real goal is to re-do that aforementioned failed experiment properly and Ret Gone the entire human race, so that they can have Earth for themselves. Oh, and the Humongous Mecha they use are Powered by a Forsaken Child, meaning that every Dolem killed was an innocent human life suddenly ending.
Except for those few like Largo which were powered by knowledgeable Mulians.
The case of Humanity vs Nausicaä of the Valley of the Wind has been opened. It engineered a vast, vast number of Weapons Of Mass Destruction, which include the titanic cyborg-like God Warriors, destroyed the entire ecosystem of the whole world, and finally all but perished in the Seven Days Of Fire. But its greatest sin was to create the Heart of Shuwa, a biological computer which contains a human-like consciousness, and which, when found by the few surviving humans, dispensed just enough scientific knowledge to enthrall them. Additionally, war technology pre-Seven Days Of Fire is still scattered across the planet, including the aforementioned God Warriors. And if that's not all, the Heart deliberately created the Sea of Corruption and the Ohmu to cleanse the planet, so its creators could live again in a purified world —after willingly destroying the current mankind.
Comics
The Celestials in Earth X created superheroes in order to act as an "immune system" against Galactus, in order for the baby Celestial gestating in the Earth's core to come to maturity. The thing is, when it matures, we die. We'd die sooner if the Earth was eaten by Galactus.
The Celestials aren't any better in the standard 616 universe. The planets they abandon for millions of years are the lucky ones. The Celestials have a nasty habit of purging all life on a planet if they don't like what they see. To make things worse, the only standard they have is whether or not the planet's inhabitants might become a potential threat to the Celestials someday. Which is pretty bad for Earth since Sue Storm managed to temporarily kill one of them. They also used our Sun to seal one of their own, considered a dangerous deviant. It turns out his "deviancy" is thinking the rest of his race are dicks.
The Merk Drizripool is definitely one in Nexus; the rest of the Merk are merely Neglectful Precursors.
Film
The unknown alien species from Supernova is smart enough to be able to encase "9th dimensional matter in a 3rd dimensional shell". This shell's energy has the effect of a Fountain of Youth when touched. (Better than candy!) The real use for this artifact? To blow up any civilization advanced enough to have developed star drive and reach the places where they've hidden these supernova causing weapons.
Literature
The Thrint in Larry Niven's World of Ptavvs (in the Known Space universe). When their empire was threatened by a successful slave revolt, they went out in a blaze of spite, sending a telepathic blast that killed almost every intelligent being in the entire galaxy - including themselves. It took a billion years for sentient life to evolve again.
One story suggests they were not only abusive back then, but they also wanted to make sure they would get any pockets hiding for a thousand or million years after. This weapon exists until the modern day, and goes off from time to time, no longer able to kill all vertebrates, just anything that is sentient... The Thrint were notoriously stupid- they relied on mindslaves for any task requiring much thought or effort. They were about as emotionally mature as you would expect from someone waited on hand and foot since birth by entire planets, too, explaining the vindictiveness.
Also humanity's ancestral Ancient Astronauts, the Pak, who would kill us all if they met us today; a fleet had to be sent out to head them off and wipe them out before they could realize what had happened to us. They're violently xenophobic, and we've mutated far too much to smell right, and our culture is too different for them to accept.
Imaginatively known as "The Builders". It was shown that they made them to defeat another alien race and things went wrong. So less abusive and more technology has turned against us. Given the kitbashed and divergent technologies of Berzerkers over the millennia of endless killing, it in unknown if one race used them as the Final Option against another or if two or more different factions or races deployed these death machines against each other. (You could always ask a berserker—but they don't care, and you wouldn't survive to share the answer...) No matter how you slice it, Berserkers are shining examples of Horribly Right as well as contenders for largest mass production Precursor Killer models.
The gods in the Dragaera universe are ascended humans. They are not very nice people, but most of their manipulations on the material plane are for the sole purpose of preventing their old masters (the Jenoine) from coming back and enslaving the world to experiment on it again.
The Wolves/Inhibitors from Alastair Reynolds' Revelation Space novels seem to be this. They deliberately transformed themselves into (usually) nonsentient machines which act to prevent sentient life from spreading through the galaxy—typically by way of genocide, though they're sometimes willing to overlook planetbound life-forms. They do have a noble-sounding motivation—they're trying to ensure the collision with the Andromeda Galaxy doesn't wipe out intelligence permanently, and don't believe a multiple-species society can pull together to prevent the chaos ahead—but they've been slaughtering for billions of years, there are billions more to go, and it's questionable whether they really intended to end up this way.
Some of the shrouders are pretty abusive too; the one time they didn't kill or drive insane any human that got too close to their territory, it was part of a plan to trick humans into awakening the Inhibitors, so that the shrouders would know whether it was safe to come out of hiding. It wasn't safe, and humans were driven nearly to extinction as a result.
New abuses added with every new novel. Some are negligent, some are abusive. They took the Space Elves and made them unable to kill, but did nothing to their instincts to dominate and control, so instead they seek economic domination of everyone. They convinced most of the other races if they wish to ascend they have to be Perfect Pacifist People, knowing this is not only false, but other races who use rage in their mental powers exist and are actively looking for races to use as cannon fodder and slaves. They also convinced those child races that modifying a race against its will is a good thing, and they are doing it to humans. Oh and then there is the Posleen, where they took a race that was something like Ancient Greece and made them into a Horde of Alien Locusts by making them breed often and quick, and so that 9/10 would be born with a form of mental retardation except for genetic memories and gifts for things like agriculture. And when this went horribly wrong they tried to shove them off on a prison planet, and after they escaped It Got Worse as they started to actively harm them to try and contain them more. Like wrecking their cultural memory so instead of actively looking for their foes, they loot and breed and plunder everyone.
In the Uplift series, the punishment for being Abusive to your client species is often extermination. Also, way back in prehistory, there was description of a group called "The Lions" who ignored the rules, ruled without any care of the potential species for millions of years (causing mass extinctions, which for the Galactic Society of the Uplift universe is tantamount to genocide), destroying lots of information about the past, and had to be put down by an alliance of Sentient Species which would have to rebuild so much lost information on Galactic Civilization and put in new safeguards.
An idea of the scale involved is that the Lions ruled the Five Galaxies for twenty million years. In retrospect this is seen as a brief, nasty interregnum.
The Silastic Armourfiends of Striterax, the most violent race in galactic history (Their army was named something even more horrific), built the supercomputer Hactar for the sole purpose of designing a bomb that would destroy the Universe. Also were indirectly responsible for the people of Krikkit launching their millennia-long genocidal galactic war. Estimated casualties: Approximately two Grillion.
The Shaddill from The League of Peoples Verse travelled around "uplifting" deserving species by granting them wonderful gifts of sufficiently advanced technology... gifts which would destroy the species' culture, stagnate their development, and slowly drive them into decay and extinction.
The Stormlight Archive has the Knights Radiant, who turned on humanity for an unknown reason. However, while they are definitely seen as this by most of the people in the series, they might not actually count.
There are four major races of precursors in the Malazan Book of the Fallen, all of whom fit this to a greater or lesser degree:
The K'chain Che'malle, the oldest race, were [[Lizard Folk lizardmen]] who ruled the planet with an iron fist; when Che'malle survivors show up in the last couple of books, though, they turn out to be more coldly alien than evil and end up allying with the protagonists, recognizing that humans are now the dominant race on the planet.
The Jaghut were mostly a race of solitary, pacifist scholars and mages, but every so often one of them would go mad and become a Jaghut Tyrant, effectively a God Emperor to the younger races they enslaved.
The Forkrul Assail are the most clear-cut examplel; a race of Knight Templars obsessed with purity, they killed their own god when it didn't live up to their standards, and come back in the last couple of books to give humanity the same treatment.
The T'lan Imass are an undead Neanderthal-type race who are dedicated to destroying the Jaghut to prevent any more Tyrants from arising. They don't have much to do with modern humans (except for the Logros T'lan Imass, who got recruited by Kellanved as shock troops), but historically they have been known to wipe out whole nations if they see a need.
In John C. Wright's Count to a Trillion, the precursors left the Momument, so that we would meddle with it and reveal our existence, so they could come to enslave us.
Live Action TV
The Ori from Stargate SG-1 who fought and chased away The Ancients. Both are the same race, just different cultures.
The Ancients can almost be considered to be abusive due to their extreme, if not outright sadistic level of negligence, when ascended and otherwise. However, despite the extremely lengthy case against them, the Ancients really do believe that their lack of action is preventing something worse.
Before their society was founded, the Time Lords were pretty evil. They would kidnap species from different planets and have them fight to the death for their amusement.
The Time War was not a positive influence on the Time Lords' disposition. They became so unpleasant and genocidal that the Doctor had to basically turn all of Gallifrey into a Sealed Evil in a Can.
The Silence. They manipulated humanity in secret for millennia and not for good ends. They've been actively trying to save the universe from a future threat that apparently involves the Doctor. To achieve this, they've kidnapped the baby daughter of the Doctor's companions and tried to raise her an an assassin. Admittedly, this plan seems to have failed. They also even admit that we should kill them all on sight.
The Vorlons and Shadows from Babylon 5, who manipulate younger races to prove a point to one another. When that isn't going well enough, they start blowing up the races who don't agree with their point of view. Made worse by the fact neither of them can really remember why they are doing what they are doing anymore.
In Go-onger, an ancient counterpart of the villains known as the Horonderthals caused the dinosaurs to destroy themselves.
The Greys of The X-Files. Where to start? They manipulated some of the most powerful people on Earth into plotting against the rest of humanity (turning us against each other), abducted and performed medical experiments on us, plotted with their human allies to cover up their existence, leaving said abductees as social outcasts, planned to use the Black Oil to enslave us until we were no longer of use to them, at which point they planned to make us extinct, touched off a war with a rebel faction that was fought on Earth and resulted in tragedy for the families of their abductees, sent the Mighty Morphin' Bounty Hunter and the Supersoldiers after us, and by the way... their invasion date is still set for 2012. Even then the real villain is "Black Oil", the creature(s) who took over the originally-peaceful Greys.
On a much, much lesser scale, Mayor Wilkins also counts. He created Sunnydale for the sole purpose of creating a feeding ground for demons so that he could become a pure demon himself.
Star Trek's Iconian civilization was apparently so abusive even in their own time that the other races at the time banded together to wipe them out, and are always referred to in leftover artifacts as "The Demons of Air and Darkness".
In Star Trek Online, the Iconians Aren't so extinct and apparently have been involved in The destruction of Romulus, and the Undine and Borg issues plaguing the Alpha quadrant as of late.
Ancient peoples lived in a very dangerous world. Their gods were rarely nice. Often, they were vicious bastards.
Tabletop Games
The C'Tan of Warhammer 40,000 definitely fit the bill, having had a massive war with the (merely neglectful) Old Ones, and given the galaxy the Necrons.
40k being whatitis, of course, they both lost. Once galaxy-spanning races, in the game's current setting both races combined have five people left.
The Illithids (Mind Flayers) in certain incarnations of Dungeons and Dragons. Squid-headedbrain-eating power-hungry masters of a multidimensional empire brought down by their own slaves.
At least one story suggests they are actually thrown out of time. In one source book dealing with different blood ancestry gifts (stuff like having dragon descendants, etc.), Illithid blood powers are in the people who are the Illthids' ancestors. Thus, some humans are Abusive Precursors.
In the fan-made Aielund module series for Neverwinter Nights, the mind flayers (called Saquarin, but they use the same models and rules) are aliens who keep 'lesser races' as cattle without them knowing it, and have Githzerai agents on the planets to engineer wars so as to keep the humans (and others) technologically inferior.
Ironically, this is a terrible plan. Some of the greatest advancements in human technology come from trying to develop ever-more-lethal means of killing each other.
Aboleths used to have a sprawling empire at the dawn of time, or maybe even in the previous universes. They have very little use for anyone not a slave or an experiment.
The Primordials of Exalted were often described as being destructive jerks who, when not consumed with the Games of Divinity (AKA the Magical Crack Xbox), would travel the world, messing things up for their own amusement and create hideous monstrosities and crazy concepts alongside the more normal things in the world, and tasked the gods with the job of fixing things after their destructive romps. Eventually, the highest gods got fed up, empowered mortals to defeat their overlords, took over Creation, and took the Games of Divinity for themselves. That being said, the highest gods aren't exactly doing a good job, and now the Primordials have actual reasons for trying to break things.
Mildly justified from the Primordials' perspective in that a safe place to kick back and relax from the constant struggle against the chaos of the Wyld was precisely what they created the world to be — without them, all of Creation including the gods wouldn't even exist. To them, the gods' revolt must have been roughly equivalent to building your own clubhouse and, after having fun there for a while, finding that your furniture has decided to kill you, and somehow made the sandwiches able to.
'Justified' is one word for it. Another might be 'sadistic'. They designed the entire human species as living Essence generators, designed them to transmit that essence through prayer, and introduced the concepts of fear, pain, and uncertainty into their design, while at the same time constructing them in a manner that is massively underbuilt to the task of individually surviving the rigors of the world... an issue only offset by their rapid reproductive cycle. All of this was done expressly to make them pray more. The closest metaphor would be the act of genetically engineering a tree that produced more fruit the more pain and cruelty its caretakers subjected it to. Again, one would have to make the tree capable of unambiguously feeling pain in this process. The act of creating a sapient species for the singular purpose of capitalizing on its suffering cannot be counted as anything other than malevolent cruelty.
Then again, sapient beings are necessary to keep Chaos out of Creation (it has something to do with imagination and how the Fair Folk hate imagination). Thus, humanity is like a Great Wall of China that can feel pain.
That's not quite right... The Fair Folk are chaos incarnate, and thrive on imagination and emotion. The existence of life forces a sort of order, at least on a metaphysical level. Though, admittedly, imagination could be argued to be part of it too, some Fair Folk don't want to destroy creation precisely because it is so amusing and a great source of stories.
The Titans from Scion certainly fit the bill, the Gods rose up against them because they were horrifically abusive and locked them away.
The Scarred Lands setting (also by White Wolf, who are obviously in love with this trope) has ostensibly the same backstory. There are hints that the Titans may eventually, even inevitably return to power, that the entire 'reign of the gods' is just the cyclic stage of the particular Titan Denev, who is relatively benevolent.
The Ancients in Traveller. As they have kidnapped creatures (including humans) from Earth and sowed them on other planets that makes them a bit like The Grays, as well. The most abusive of all by far is the first Ancient, Grandfather, who uplifted the other Ancients, gave them his abusive guidelines to follow, and wiped them out when they finished what he wanted. Oh, and he's still around, watching and waiting.
Video Games
The Rakata in Knights Of The Old Republic enslaved every other species they came across. Ever wondered why Tatooine is a Desert World? Well... They also left behind the Star Forge, a colossal space factory capable of singlehandedly sustaining the war effort against a galaxy, powered by The Dark Side, designed specifically for aspiring Galactic Conquerors. Complete with operator's manual. Seriously.
The Reapers of the Mass Effect trilogy seem to be trying to set the record for the most abusive of them all, and doing a damn good job at it. They deliberately left Lost Technology around for future species to find to encourage them to evolve along the lines they want — thus making it easier to completely obliterate them when they return to 'reap' what they have sown. Bonus points for not having any clear reason for doing this, several sources and characters state it is probably impossible for organic beings to understand anyway. Further bonus points for evidence in the game hinting at how long their Gambit Roulette is already going on: At least 37 million years, with a purge of every sentient life at appropriate Tech Levels every 50,000 years or so. Did we forget to mention that their mere presence causes absolute mind control that is shown to be completelyirreversible? Few of their victims ever muster the massive amount of willpower required to kill themselves first, so at this point death is clearly the nicest thing they can do to you.
And that appropriate level isn't space-faring, either. Evidence in the sequel hints they carried out an orbital bombardment on at least one race that had developed only Bronze Age technology.
Actually if taken at face value what is said on the planet Klendagon's information sheet, that is thirty-seven million years in human measurement, or that 37 million years ago was the last time anyone had any power to stand against the Reapers, and obviously, ultimately lost. Confirmed to have been caused by an anti-Reaper weapon in Mass Effect 2.
Even more shockingly, the rift was made 37 million years ago, but the weapon must have been fired even earlier. Remember, projectiles travel at sub-light speed, so we may be talking untold extra millennia.
It is possible that we may never know how long the abuse has continued. The only reason evidence was found on Klendagon to begin with was that a massive portion of the planet had been carved out, a feature impossible to erase. The Reapers have shown a tendency to leave only fragments of civilizations and any traces of civilizations prior to Klendagon have likely been completely destroyed by the intervening scavengers, erosion, and other depredations of time.
The sequel shows that the Reapers are perhaps far more abusive than anyone realized.The Collectors? They're the remnants of the Protheans, mutated beyond recognition and forced into mindless, torturous servitude. The deadly-to-everything-but-humans plague that Mordin was trying to cure? A weapon the Reapers were taking for a test drive to isolate humans. The husks? Test models for the final boss: an embryonic Reaper made of an alloy of space age metals and tens of thousands of liquefied alive humans. At this point, flat out annihilation is actually one of their nicer feats.
The plague is described as causing increased randomization in the genetic coding of the affected species. Combine this with the implicit diversity of humanity (which makes them excellent test subjects) and you realize that the plague is most likely trying to create more species viable for reaperfication.
The ending of that game sheds more light on what the Reapers actually want: they were created by a being (probably a powerful AI) known as the Catalyst to prevent races from advancing enough to create synthetic life: if they did, it was believed the synthetics would eventually rebel and wipe out all organic life. The Reapers would invade every once in a while, harvesting any sufficiently-advanced races and turning them into Reapers while leaving the lower species alone. Given that they're preventing the death of ''all'' organics (for a bit), this might just redeem them very slightly. Maybe.Not really.
ME3 also reveals that the Protheans were pretty bad as well. They ran a galaxy-wide empire, subjugating other races (if they didn't exterminate them first) and absorbing them into their culture. Their reasoning was that, with the threat of synthetic life on the horizon (represented in their cycle by the Zha'til and the Metacon War), all organics had to stand together or perish. Once the Reapers came upon them, they tried nurturing primitive species, hoping that some Protheans could sit out the destruction in stasis and emerge after the Reapers had left to lead these species against the next cycle. Their best hope were the Asari (who, ironically, ended up running the galaxy themselves with wisdom, patience and diplomacy), but they also intervened upon the Hanar and at least studied some of the early humans. It's also memtioned that they served Salarian liver as a delicacy.
Not as bad as the Reapers, but the quarians are this. Long ago, the geth were created by the quarians as a slave race, but as they improved the geth's inteligence, the geth began to think outside the box and ponder the world around them. It came to a head when a geth turned to it's master and asked "Do geth have souls?", and it's implied that this wasn't the first time this happened. The quarians became quite freaked out by this and decided that all the gethshould die. A war began between the quarians and the geth, and it didn't go well for the quarians: most of them were killed, and they had to flee their home planet. Whether or not they deserved it is up for debate.
New information in ME3 makes it a more deserved result: not every quarian agreed with the 'destroy the geth' course of action. The geth-sympathizers were killed by other quarians, and only then did the geth decide that their makers had to be kicked off-world for now. It is also notable that they were just kicked off-world; it is explicitly shown that the geth had the power to wipe out the quarians completely, but chose to be merciful, by letting the 17 millions last quarians survivor go, but the geth choose peace as soon as it becomes an option.
The Dnyarri in Star Control/Star Control 2 are the primary cause of the Ur-Quan's actions, both Kzer-Za and Kohr-Ah. And no, they were not nice people. For a better perpective, they were inspired by the Thrint in Literature above... and then were made even worse.
If you want to consider Star Control 3, let's put up the Eternal Ones. Seeding the universe with sentient life so you can eat all of it? Considering that one such sentient population managed to figure out a way to make sure that no one has to die in their iteration, while the Eternal Ones went through who knows how many iterations committing universe-scale xenocide...
The Sarrukh "Old Ones" in Neverwinter Nights. Powerful magical humanoid reptiles forced into dormancy by a cooling climate... for now.
Elaboration in the tabletop game revealed that the Sarrukh, one of five Creator Races, had begun fairly non-abusive, but (mostly) began to slide into evil as their god fractured and fell into somnolence and an excuse was made for sacrificing non-Sarrukh (sacrificing honored volunteers are one thing. Mass sacrifices of slave races, another).
Considering the events in the Starcraft II campaign, it seems that the Xel'naga, who were originally portrayed simply as Neglectful Precursors (for creating the Zerg and getting destroyed by them), are probably still be around, and may have orchestrated the entire Zerg invasion, implanting the Good All Along Overmind with an Obstructive Code of Conduct to assimilate the Protoss, thereby enabling the creation of the Zerg-Protoss Hybrids that the Xel'naga had originally wanted.
However, there is some evidence that this was actually hijacked by a third party called The Dark Voice, who was sealed away by the Xel'naga and may or may not have been a renegade Xel'naga. So this may get the Xel'naga off the hook, and puts him right on it instead.
The Suul'Ka in the Sword of the Starsbackstory, corrupt, gone-mad-with power Liirian elders who enslaved the Liir, used their pawns to destroy the old Morrigi civilization and killed 90% of their male population, and created the Zuul, a genocidal race of religiously fanatic Super Soldiers. The Liir retro-plague wiped most of them out, but the sequel revealed that seven of them survived and recovered... And now they are back. And they are angry. They're so bad, that isn't even their actualname: It's the Liirian concept of "abominable", (lit. winterheart, sociopath).
Sin/Yu Yevon in Final Fantasy X is a prime example. It's a Space Whale that originated as the most powerful summoner in Spira, who turned himself into a Weapon Of Mass Destruction to defend his people and ended up so hopped up on the power that he kept the summoning going for a thousand more years. The "Precursor" part comes from the fact that his daughter organized a religion based around worshipping his name and appeasing him by throwing aeon after aeon at him, so he'd always have a new host to possess...at the cost of the summoner's life.
The throwing Aeon after Aeon at Sin had the slight benefit that it prevented Yu Yevon from ever controlling a host long enough for it to lose all conscience and go on an unstoppable global rampage, wiping out all life. Naturally, the few who know the secret get understandably upset when the only means to force Sin to reboot is killed.
The Dread Lords of Galactic Civilisations II. There were two Precursor factions (the other called themselves the Arnor), one which wanted to befriend all the younger races and one which wanted to enslave them all. Guess who's who. Guess which ended up as Sealed Evil in a Can.
The Precursors who built the Sphere in Prey seeded countless planets throughout the galaxy and are directly responsible for life on Earth. And all they ask for in return is that every few thousand years, they stop by and gruesomely abduct and slaughter countless people to keep their Organic Technology running.
The creator of the world in Legend of Dragoon created a Tree of Life, each fruit of which is a new species of animal. Apart from the sapient species, these creatures are uniformly hostile to all life, and the final fruit, the Virage Embryo, exists for the sole purpose of destroying all life on the world.
The H'riak in Alien Legacyseeded aggressive life all over the galaxy, designed to hate and destroy all non-H'riak life. The Centaurians are one such race. When they found humans, the first thing they did was attack, starting a war that resulted in most (if not all) life on Earth to be wiped out, leaving only colonies. The H'riak also seeded the two habitable planets in the Beta Caeli system with violent flora and fauna and created a race of psychiccalamari who, while not aggressive, try to kill humans because our thoughts hurt them. Also, the ship they send to Beta Caeli is also capable of causing the star to go nova as a last resort.
The plot of Ares Extinction Agenda can be summarized as follows: Some alien(s) all life in the universe. Said alien(s) have decided humanity is destructive and wasteful and should be wiped out. A robot humans built disagrees, strongly.
Done by humanity itself by accident in the Mega Man Legends series. See, humanity made an artificial slave race called the "Carbons", and to make sure they didn't go rogue, set up several failsafe systems to wipe out all the Carbons if there were any signs of acting outside usual parameters, or if Carbon population was suddenly much greater than the human population. Then the humans died off of natural causes, leaving behind the sapient carbons and several failsafe systems that thought the carbons had gone rogue, when they in fact were simply living.
For the breadth of Phantasy Star Universe and its several expansions, the Ancients are just MacGuffin providing story fodder. Then we finally get to meet a pair in Portable 2 to find that just like the current generation, they ran out of resources fighting off the SEED , and subsequently sealed themselves away in subspace. In a nice long Evil Planthey left humans to keep the system spruced up and ready for colonization via enforced Mind Fuck when they reached the ability to use subspace. About the only reason you have a chance in hell is because one of them is a Benevolent Precursor.
For millions of years in Otherspace, the god-like Kamir and Hivers fought each other with willful disregard for the destruction they were doing to the rest of the universe, often pulling players in as proxy warriors in their machinations. Eventually, all their destruction ended up breaking the universe.
Novels in the HaloExpanded Universe reveal that the Precursors tried to exterminate the Forerunners... and so the Forerunners struck back and wiped them out instead. Also, it's heavily implied that the Precursors either created or became the Flood.
Most fans of the games are under the impression that the Forerunners were a noble society of peacekeepers that made a Heroic Sacrifice to save the people of the galaxy, the only mistake made being their ability to keep the peace so effectively that nobody needed to evolve. Wrong! They were actually racist supremacists who de-evolved their enemies' children, did everything they told everyone else not to do because they were the "Chosen Ones", and tossed countless sentients to the Flood to see what would happen. How many actually gave a crap about anyone else? So far, two. Maybe.
The Black Moon in Galaxy Angel has become this either by corruption of its programming into being a factory of destruction or because it was built that way from the start. This makes the White Moon either its counterpart or its opposite. Even at the end of the first game it's not very clear.
In Might and Magic VIII, a non-malfunctioning Ancient construct, Escaton tries to destroy the world. As there doesn't seem to be any reason for that, this would appear to make the Ancients fit into this trope (especially as they are still out there, just rather busy at the moment)... but as it turns out, there is a reason: the Ancients, rather reasonably, put failsafes into Escaton to keep him from being subverted by the Kreegan, one of which was an inability to willingly stop destroying a world once he had started. As he only started doing it if he deemed a world unable to defeat the Kreegan, that generally worked out, but in this one case he happened to underestimate the inhabitants...
The FreeSpace series has the Shivans, though why they are so intent on destroying the Terrans and the Vasudans is a complete mystery. That is, until the end of the first game, where it's revealed that they do it to protect other lifeforms in the galaxy, even though this is also merely a guess at their real intentions. The second game postulates that they're a race of Sufficiently Advanced Aliens from another universe and are trying to get back home. The Ancient Ones were pretty bad too, either enslaving less advanced lifeforms or running rebellious/resisting races into extinction, which caused the Shivans to wipe them out entirely. It's also implied that the Ancient Ones had a hand in helping the Vasudans get off the ground, and that the Vasudans rebelled just as the Shivans began attacking, thus allowing them to continue to grow until they met the Terrans, who were probably ignored by the Ancient Ones because of the Shivans' wiping them out. To give them credit, the Ancient Ones also left behind artifacts on their home planet in the Altair System that helped the newly founded Terran-Vasudan Alliance defeat the Shivans in the first game by destroying their super-destroyer, the Lucifer, while in Subspace transit to the Solar System, to destroy Earth like it had Vasuda Prime before it.
On balance, the X-Universe's Ancients are this. Theoretically they have good goals, such as preventing the heat death of the universe, and they consider the Portal Network they built a gift to the younger races. Unfortunately they have a tendency to think of the younger races as a single group, making them frighteningly willing to toy with them seemingly at random. Since their most direct method of manipulation is to switch gate pairs in the Portal Network, this means they do things like start interplanetary wars, separate colony ships from their home planets or lock fleets in deep space with nowhere to go, or even turn off the whole network. Then again, the network shutdown came partly in response to the Xenon gaining control over a sizable portion of the galaxy, so YMMV.
Web Original
The followers of the Old Ones, ancient space gods from another dimension, were the first lifeforms to colonize a primordial Earth of the Global Guardians PBEM Universe. A series of wars begin with the Old Ones on one side and U'tua the Gardener, the war-fleets of five of the Progenitor Races, and at least thirty of the Progenitors' more advanced client species, on the other. Eighteen centuries of constant warfare culminated in the banishment and imprisonment of the Old Ones to places outside the universe. The victory came at a great price, as the entire H'ch'wee and Krang species, along with every member of their various participating client species, were exterminated in the fighting. Unknown to the victors, a small number of servants of the Old Ones survived on Earth. They went into hiding deep underground.
The Great Old Ones (yes, thoseGreat Old Ones...) in the Whateley Universe. They fought a war with the Sidhe that wiped out the Sidhe and got the Great Old Ones sealed out of this dimension. For now...
The court would like to bring to evidence the precedent set in previous issues. One, that the Great Old Ones plead guilty, except they have no concept of guilt. Two, they would like permission to eat the buffet, also known as the jury.
Web Comics
The Titans from Erfworld built the eponymous universe with laws of physics which seem designed to make peace impossible. However, recent events indicate they may be still active.
Whatever created Sburb in Homestuck: the game in question seeds species' existence for the sole purpose of destroying it except for a limited group of children who are tested to see if they can win a difficult game. And the children don't even come from that planet, they're created by the game itself. The trolls wanted to become this to Earth. Didn't quite work out.
In Transformers Prime, Unicron is this for all life on Earth. He IS planet Earth (or at least, the center of it), and views the organisms that have come to live upon him while he slept much the same way as if you or I were to wake up covered in mosquitoes.
Real Life
The "Deadly Probes Scenario", one explanation for the Fermi Paradox, is along these lines - there aren't any aliens because some ancient alien race released robots programmed to seek out and destroy intelligence. Mentioned here.
