Every time it looks like another race, usually the Tau or Eldar, is starting to look more sympathetic than the dictatorial (among other things) Imperium, they'll start pulling off new atrocities in the next edition. In 40K, about the best you can hope for is a Well-Intentioned Extremist or Knight Templar who won't kill you too painfully.
On a general scale, you can't find any faction that is good by our standards, but some sub-factions and characters, like several Space Marine chapters, a few Imperial Guard regiments, the occasional Craftworld Eldar protagonist, Ravenor and Ciaphas Cain(HERO OF THE IMPERIUM!) or the Tau count as good. Unfortunately, they are far outnumbered by less moral groups, Bad Bosses, people who gotoo far for their cause, and the Dark Eldar, Necrons, Tyranids and the forces of Chaos.
Again, its not as much as normal "Good" as much as "being nicer and more rational than those around" or (at least slightly) caring about (their own) civilians and collateral. Tau is your typical militaristic expansionist state. Cain did admit that he actually shot a number of his own troopsnote For incompetence of all things, absolutely abhors Xeno races and "traitors" note Humans that decided that Greater Good suits them better than rule of the Imperium. Often they weren't exactly given a choice and sees nothing wrong to use criminals for target practice in military orphanage.
It is saying something about the setting when you consider the "good" factions of the game: arrogant space elves who view humans as little better than filthy, stupid animals; the Imperium of Man which is an Anti-Heroat best, but would easily fall into villainy in most settings, where their policy against all aliens is shoot first, talk later, and they destroy entire planets of people if it is suspected to have a substantial corruption of Chaos, not to mention that their oppression is nothing short of fascism; and the communist Tau Empire, whose leaders are powerful psychics that control their followers through mind control and their MO is "join us and serve the Greater Good, or we'll kill your entire race". That said, at least Tau bother with allies, the Eldar leave you alone unless you come up in one of their schemes, and the Imperium is fairly tolerable of you as long as you're human and believe in the God Emperor. Which is more than we can say for Chaos, Orks, Necrons, Tyranids, and Dark Eldar.
It's also probably worth mentioning that the comedic relief in the series is the Orks, a race of Ax-CrazyBlood Knights, who are hellbent on attacking and destroying as many worlds as they can, just because they love a good fight.
In Genius: The Transgression, the Peerage deliberately chose to be Grey because if you have a Genius go off on his own he'll often become Illuminated, and if the choice is between accepting jerks or have them wander off and turn into Mengele, you'd better get used to putting up with jerks. The Storyteller is advised to keep the players wondering whether the Ancient Conspiracy Lemuria is really that bad compared to the barely human nutbars in high-up positions in the Peerage. (The "black" role here is played not so much by modern Lemuria, which is just going through the motions, but by Clockstoppers, the Illuminated, and the occasional Hollow Earth Nazi or Phantom Slaver Yeti.)
In Call of Cthulhu, the heroes are insane and the villains are even more insane.
The Zodiac Order are esper supremacists that want to set espers up as a the new master race and do not care about how many people have to die for that to happen.
Abraxis conducts horrific experiments on humans and espers and is ruled by a board of directors that is completely profit-driven to the point of being totally amoral, which itself is headed by a violent psychopath that frequently has entire families killed for the sake of convenience.
The Shop regularly kidnaps and forcibly indoctrinates US citizens through torture, is not above purging any witnesses who happened to be in the wrong place at the wrong time, and makes a point of isolating its espers from one another.
Eschaton is straight up committing genocide against espers whenever they can and has all of it's espers (all of whom are devoutly religious) convinced that they're demon-possessed.
The Red Orchestra is basically the psionic KGB. They want to establish Russia as the new dominant superpower and will happily use torture, mind control, and every other dirty trick in the book to do it.
Aleph is a cutthroat secret society fronted by several Asian corporations. They want to increase their economic power, no matter what the cost. They're similar to Abraxis in terms of their methods.
Though there are heroes in Eberron, they are few and far between. In the core Eberron setting book, there's only 1 high-level Good NPC, and she is a young girl who only has such power while in the same city as the Silver Flame (a metaphysical source of elemental good) itself. And that person is responsible for trying to make sure her church full of Knight Templars doesn't cause too much death and destruction. Of course, Word of God from the setting's creator indicates that at least part of the reason for lack of powerful good NPCs is to keep the focus on the PCs as the heroes.
All of this said, while all of the major mortal factions (major nations, dragonmarked houses, and even the Blood of Vol, a creepy religion secretly controlled by one of the setting's Big Bads) are more-or-less amoral, few of them are of the Card-Carrying Villain variety- most of them simply have their own agendas that they're interested in pursuing regardless of who gets in their ways. Unfortunately, there are several extremely power supernatural forces that are unambiguously evil (Lords of Dust, Dreaming Dark, and Daelkyr being the three biggest) and would pretty much destroy the world and/or reshape it in their image if they had their way. Really unfortunately, all of these are creepily good at disguising their true nature and working through pawns who may actually believe they're the good guys, and the main forces capable of opposing them on their own level are morally ambiguous in their own right (the dragons, the Undying Court) and the one that is purely good (the Silver Flame) is inherently reactive rather than proactive, and influential parts of its religion have gone the Corrupt Church route.
Cthulhu Tech: A crossover between H.P. Lovecraft and Neon Genesis Evangelion was bound to be pretty hard on everybody — an ongoing theme of the setting is how the horrible, soul-rending evils wage a tireless war to keep the really bad stuff at bay. To quote the Corebook's intro fiction: "Some people say war is hell. Well, I've seen Hell. This is worse."
The main factions are a police state, a number of secret societies (the Eldritch Society, the Children of Chaos, the Esoteric Order of Dagon), and the Rapine Storm (who are significantly more evil than they sound).
The Necessary Evil setting for the Savage Worlds game-line starts out with all the superheroes of the world getting killed by a precision strike by invading aliens. The only ones left to oppose them (the PCs and their allies) are the supervillains.
Winterweir is an Anti-Traditional Fantasy RPG in many respects. As such, the Trow and humans killing each other are more likely to be decent people suffering Fantastic Racism than not.
BattleTech does this a lot as well. The state usually tagged as the good guy, House Davion, was led for years by the Magnificent Bastard to end all Magnificent Bastards, Hanse Davion. A man who engineered a massively destructive war and faked the brutal cashiering and disgrace of the son of his best friend and intelligence adviser... all so he could gain revenge on one man. Yet this same state is (almost legitimately) the beacon of freedom and rights in the Inner Sphere.
Granted, the 'one man' he wanted revenge on was the leader of another Successor State, who very nearly managed to actually replace Hanse with a brainwashed doppelganger who'd have acted as his willing puppet. All events laid out in the (very early and thus possibly now somewhat obscure) BattleTech novel The Sword and the Dagger. Wars have historically been fought for less...
Or ComStar, who are shown to be a manipulative and secretive organization, that can easily bring a state to its knees just by shutting off all communications between planets, and which is not above intriguing to keep its own interests secure — there are a few hints that the Succession Wars may well be an Evil Plan by ComStar intended to preserve its own autonomy and power within the Inner Sphere. At the same time, it is the last holdout for many destroyed technologies that humanity would need to survive and thrive.
When you have the likes of Word of Blake, a fanatical, genocidal splinter faction of the aforementioned ComStar that retained its pseudoreligious trappings, even the likes of the Capellan Confederation—long regarded as one of the least cooperative Successor States—looks good. Having decidedly one-sided caste based citizenship, the most ruthless secret police and special forces units around, and the occasional tendency to double cross allies for their own gain doesn't look quite so bad next to the World of Blake nuking, orbitally bombarding, chemical spraying, and bio-bombing entire planets into dead worlds.
The Dungeons & Dragons campaign world Greyhawk lives for this trope. The world of Oerth is always on a knife's edge between Law and Chaos, and there is an organization led by Mordenkainen the Mage (who must people will recognize because his name appears on a few spells) that ensures that neither gains ascendancy... by any means necessary. Mordenkainen, in canon fiction (Word of Gygax, however, has it that this wasn't intended originally, had he not been ousted from TSR) will work with the Big Bad one week, and then lead a group of paladins against him the next... all to keep the balance between Law and Chaos correct.
So does Dark Sun. A Death World reduced to a scorched, mostly lifeless desert of rocks and dust (the ocean has been renamed the Sea of Silt... take a wild guess why they call it that), where there isn't one creature (or plant) that isn't dangerous in some way (a sandcrawler looks like an adorable, fluffy, foot-long black furry caterpillar... it uses its cutesy appearance to get close to people, waits until the poor fool falls asleep, then implants its parasitic larvae in their flesh), one of the facts emphasized is that people will do terrible things merely to survive. That this is a Justified Trope for the setting goes some way towards explaining why it's a Crapsack World.
The city of Neverwinter, which has its own campaign book as of 4th Edition. Sure, you have the standard Obviously Evil factions such as the Abolethic Sovereignty, Thay, the Ashmadai, and a criminal empire of wererats, but even the "good" factions don't come off particularly well. Lord Dagult Neverember is unquestionably helping the city recover after being ravaged by an erupting volcano, but he's a bit of a sleazeball and his reasons for devoting resources and money to the city aren't entirely altruistic. And the Sons of Alagondar, while certainly well-intentioned in their desire to see Neverwinter back in the hands of its people, are willing to murder, riot and hop into bed with the Dead Rats and Thay in order to see their goals achieved.
The Solar Exalted are the returned God-Kings of yore, who once went mad from the Great Curse and were executed en masse, with their souls trapped in the Jade Prison so they wouldn't reincarnate and continue their reign of terror. On the one hand, they seem to be a lot less insane now, and the world desperately needs their help, but there are plenty of folks who are worried they'll go back to their old habits...
The Lunar Exalted have spent their time since the Usurpation on the borders of Creation, subtly influencing mortal affairs and engaging in social experimentation to create societies that do not require divine or Exalted intervention to function. Unfortunately, most of the elder Lunars that are running the show are selfish, evil, or insane (or some combination thereof), and younger Lunars have to follow their orders or risk losing access to the moonsilver tattoos that will prevent Wyld taint.
The Sidereal Exalted are in charge of maintaining Fate and keeping causality intact throughout Creation, but they also have a bad habit of sticking their nose into mortal affairs for the sake of their political agendas. The Usurpation was their idea, as was the Dragon-Blooded Realm, and they constantly squabble over whether they made the right choice or not. With the Solar Exalted back, the old factions have stirred up again, with some welcoming their new Solar overlords (while trying to maneuver themselves into becoming The Man Behind the Man), and others violently opposing their return.
The premise of Anathema: Either meet a daily murder quota or let the Earth and all of humanity die a slow, horrible death.
Eclipse Phase: Firewall do some genuinely horrible things for the greater good, most of the factions have at least some dirty laundry...and they're still better than most exhumans and the TITANs.
When playing Infernum, it's either this or Evil Versus Evil. You have an order of literalKnight Templars who want to exterminate all demons in Hell, the so-called Free Tribes (which are humans who survive in Hell by being willing to do anything to survive, including using Black Magic and committing cannibalism), Fallen Angels and even idealistic demons who want to rise above their innately twisted, aberrant natures but are hampered by the limits of their biology and mentality (for starters, they can't survive without feeding off the pain of souls because it's all that holds their own souls together, and love isn't a natural emotion for them to feel). Versus these you have... well, all The Legions of Hell, who embrace corruption, torture, degradation, backstabbing, ambition and malice as the only things that matter.
In Bleak World This is essentially the rivalry between the Blackwood Company (who own street gangs, the prison system, and the media) and The Dark Skies Corporation (Who lobotomized an entire army to put demons in them and harvest the souls of the people they defend and/or prosecute.) There are many other examples, this is just the most notable.