"Among the Alps and Pyrenees, perhaps, there were no mixed characters. There, such as were not as spotless as an angel might have the dispositions of a fiend. But in England it was not so; among the English, she believed, in their hearts and habits, there was a general though unequal mixture of good and bad. Upon this conviction, she would not be surprised if even in Henry and Eleanor Tilney, some slight imperfection might hereafter appear; and upon this conviction she need not fear to acknowledge some actual specks in the character of their father, who, though cleared from the grossly injurious suspicions which she must ever blush to have entertained, she did believe, upon serious consideration, to be not perfectly amiable."
In some stories, the good guys are squeaky embodiments of shiny goodness and fight bearded stage magicians who cackle a lot. Then again, sometimes you have stories where your caped crusaders largely go up against the misguided and distraught. Other stories might have the pragmatic freedom fighters against a government who alternately sing orphans to sleep or murder their kittens. Still other stories have the world's mightiest, most murderous, most-pants-wettingest "heroes" you've ever seen against a guy who made entire worlds into slave-states for profit and kicks.
Then you have stories like this.
Rather than discrete groups or distinct moral systems, you have a sliding scale, and all groups and characters fall somewhere between "Hero" or "Good" at the furthest extreme and "Villain" or "Evil" at the other extreme. In most cases, the people closest toward the "Hero" end of the scale will be the main characters, but they're usually not perfect (and they can become even less perfect as time goes on). Their opponents fall further toward the "Villain" end of the scale, more often than not, with some that are so close to the Villain end that they don't really have any heroic qualities.
In short, none of the groups fit cleanly into the White-Gray-Black categorization, as all of them do things both good and evil with varying degrees of frequency. This generally makes for more dynamic stories, as you're never sure if the heroes will stay on the straight and narrow or villains will keep wreaking havoc.
See also Shades of Conflict and Sliding Scale of Anti-Villains. When you've got a specific group to which this trope applies, you've got a Four Philosophy Ensemble. Compare The Good, the Bad, and the Evil along with White and Grey Morality. Contrast Evil Versus Evil, where nothing is good or morally ambiguous about the characters. Also contrast Good Versus Good where nobody is truly evil.
Fullmetal Alchemist - The Elric brothers and Winry are the most purely heroic characters; the heroes from the State Military are more gray, being former war criminals who want to atone for their sins; Greed and Scar are fairly sympathetic antagonists until they become Anti Heroes; there's Barry the Chopper who is the Token Evil Teammate for the State Military heroes- he's clearly Evil; finally, the other villain characters are definitely very far down toward the evil extreme of the scale. And even one of the worst villains is spared Then of course we get Kimblee.
Despite being the protagonists of the show (as well as priestesses), the Sybillae of Simoun have moralities that are all over the range. On one end, you have the innocent Limone and the truly and actively good Rodoreamon, Yun, and Morinas. Then there are the more ambiguous Paraietta, Mamiina, and Dominura, and the self-absorbed and venal Floe. The romantic leads Aaeru and Neviril and the nations of Argentum and Plumbum are a little hard to place, while the Defense Minister of Simulacrum is decidedly at the bottom of the proverbial drain.
The manga version of Chrono Crusade. Azmaria, Mary Magdalene and most of the members of the Magdalene Order are clearly heroes. Rosette's very heroic, but has a number of vices and character flaws that get the best of her; Chrono is kind and gentle but has a dark past (including formerly being one of the villains); and Satella is mostly concerned with her own goals but still shows empathy towards others. The Sinners, although being the main villains, are mostly in the gray, from Joshua (who is devoted to Aion because the demon horns on his head are making him lose his mind, but who has understandable and occasionally noble motives) to Shader (who hates violence and expresses remorse for her actions but goes along with Aion because she believes in his ideals) to Aion himself, who is a Well-Intentioned Extremist. The closest to the actual "villain" scale are the other demons, who are either beasts who take pleasure in attacking humans or soldiers sent to kill the Sinners and whoever gets in their way—but some of these are somewhat sympathetic, since many of them are simply aliens stranded on a strange planet who are struggling to survive and believe in a lie perpetuated for generations. The morality structure is explained by the mangaka as being inspired by the idea that people aren't born evil, but become evil through their selfishness.
Code Geass. There is one genuinely, unquestionably good person, Euphemia, (Shirley is debatable, because while she is certainly kind-hearted and sweet, she is only concerned about her own feelings and school life while all hell is breaking loose outside, so she can come across as somewhat self-centred). At the same time, there is one genuinely, unquestionably evil person, Luciano Bradley. Every other character falls somewhere in between, with most of the "good guys" being flawed and somewhat hypocritical, and most of the "bad guys" being either fiercly nationalistic or a Well-Intentioned Extremist.
Taken to extremes with the main character, who can be convincingly argued to fall under any moral alignment.
Death Note has a pretty wide variety of character morality-wise, and who is truly good and truly evil is often discussed by the characters and a major plot point. Some of the characters do mostly good things for selfish motivations while others do terrible things with noble purposes in mind. Pretty much any character that declares themselves completely good is portrayed as misguided or near psychotic and good luck trying to establish with any certainty who are the anti-heroes and who the anti-villains, towards the end of the story the triumphant character even makes a reflection about the subjective nature of good and evil.
Watchmen is based around this trope. Each of the major characters is based around a different system of morality, and the conflict between these different moral outlooks drives much of the story. The Comedian is a Nihilist who sees the world as nothing but a joke, and just doesn't care about right or wrong, Rorschach is an Objectivist and a moral absolutist, incapable of seeing the world in any terms other than Black and White, Dr. Manhattan is so alienated from the human experience that the very concept of morality escapes him, and Ozymandias follows a Utilitarian moral code, in which even the most evil acts act be justified if they serve the greater good.
The Sonic the Hedgehog fanfic Prison Island Break takes place in a prison, and almost all the characters are morally dubious criminals, including those Sonic allies himself with. The most obvious exception is the villain.
J.R.R Tolkien's Middle-Earth, especially in The Silmarillion. On the heroic side of things you have most of the more noble characters like Frodo, Eärendil and Beren (though, even they aren't immune from making mistakes and moral lapses) and most of the Valar who always mean well but often make misguided choices. All the free peoples vary greatly, with morally ambigous characters like Thingol, Malgor, Túrin, Mîm, Fëanor, Gollum, and Thorin hovering in the middle and with Morgoth and his directly corrupted minons at the evil extreme. However, the moral compass of the series varies between each story, with The Lord of the Rings mostly (though not completely) revolving around Black and White Morality while Black and Grey Morality dominates The Children of Húrin and The Hobbit (with shades of Grey and Grey Morality in both).
1632: The heroes range from almost pure heroism to rather questionable, the antagonists range from evil to people who could be heroic under slightly different circumstances and/or are just victims of Values Dissonance.
In Chung Kuo, there are some very upstanding characters on both sides, who rub shoulders with pure villains.
Brandon Sanderson's Elantris. Furthest toward the Hero end, you have Sarene, who's upstanding but can be a little deceptive. A little further away from the Hero end, you've got Raoden, who resorts to some practical tactics. On a good deal toward the Villain side, you have Hrathen, but he shifts further toward Hero before the story is done with. All the way down at the Villain end, you have Dilaf.
The Dresden Files. At the furthest extreme of the Hero end we have Michael Carpenter, the Fist of God, who only fights monsters, has a grand total of one recorded instance of swearing in the series proper (which was in a side story), and is all around about as wholesome as a person can be. Slightly away from the good extreme would be the majority of the series other heroes e.g. Harry Dresden, he's a generally upstanding guy with a MASSIVE case of Chronic Hero Syndrome, but isn't above a bit of pragmatism if it's necessary. More towards the middle of the scale is The White Council which is made up of plenty of Knight TemplarJerkasses but has methods which are shown to oftentimes be necessary. The main representative of dark gray is John Marcone, who is a ruthless crime boss, but ends up joining forces with Dresden more often than opposing him and WILL NOTtolerate any violence against children. As for the monsters of the setting we have any one the supernatural villains, e.g. the skinwalker whose true form's mere sight is enough to send harry into a Heroic BSOD. To Top it of we even have Blue and Orange Morality in the form of the fae.
Daniel Suarez' Daemon and its sequel FreedomTM. Apart from Roy Merritt, who earns immortalisation as a genuine embodiment of justice, the reader's perceptions of who the good guys and bad guys are is constantly changing.
The Chathrand Voyages. There's so many plots and counter-plots going on that this is bound to happen. The three heroes need to constantly reassess who they can trust depending on which evil plot they're fighting at the moment.
In David Weber and Linda Evans' Hell's Gate series both Sharonans and Aracans are a hodgepodge of good, bad and in between, although Arcana in general has many factions with different goals some of which gravitate towards the extremes of the morality scale, while Sharona is more unified and thus more uniformly gray.
Present in Madeleine L'Engle's A House Like a Lotus, with the addition that even one person is never completely good or evil. It basically boils down to "people are complicated."
Given that A Song of Ice and Fire has Loads and Loads of Characters and no clear heroes or villains, it's no surprise that the morality spectrum comes in about a thousand shades of gray. You've got extremely honorable, well-meaning people like Ned Stark and Brienne of Tarth, bastards like Gregor Clegane and Ramsay Bolton, and more Anti-Heroes and Anti-Villains than can be listed. Among the "anti-"s, fans can't even agree which ones of them are anti-heroes and which are anti-villains. It's largely a matter of perspective.
Harry Potter is somewhere between this and Gray and Black Morality. The Death Eaters are pretty consistently on the black side, but the protagonists can vary from saints to assholes.
Live Action TV
Deadwood uses this to some extent; much of the early part of Season one casts the character of Al Swearengen as the most morally corrupt character in town. That is, of course, until Cy Toliver shows up, who quickly quickly steals the spotlight as villain most evil. Al is made to look almost a hero as the result. This is possibly subverted however, as the show in general uses the morality kitchen sink, and both Cy and Al do indulge in purely "good" acts on occasion. And then George Hearst shows up in season three, a wealthy sociopath who cannot abide things not going his own way and sets about turning Deadwood into a Company Town.
BBC’s Merlin could be argued to fall under this trope. Though there are clearly characters designed to be “good” and “evil, “heroes” and “villains,” their actions are not always so clear-cut, and this has caused some Base Breakage among the fandom, especially when it comes to the often-justifiable actions of the “villainous” characters, like Morgana and Agravaine, and especially Mordred.
LOST. Most of the characters are Anti-Heroes or Anti-Villains. The show's Big Good is still a Manipulative Bastard who is the embodiment of Good Is Not Nice, and the Big Bad is ultimately given a rather sympathetic motivation (although by the time of the show's main events he is still unmistakably at best an Anti-Villain). There are only a few characters who could be considered unambiguously good or unambiguously bad characters, but the distinction between good and evil is still there, even if the viewer's perception of which characters are which is constantly changing.
While all Table Top Role Playing Games allow you to make a character who is anywhere on the map, different games have within their "default" tone different views. Please consider a game's "normal" tone and not what players might decide to do. For example, you could play a completely virtuous character in Shadowrun, but that doesn't change the fact that it's a dark and grimy cyberpunk world where amoral mercenaries work for backstabbing corporations and inhuman spirits.
Dungeons & Dragons and spin-off Pathfinder in most of its settings has this. There may be a necromancer who is repeating Mengele's work on his victims, a paladin who spends all his days feeding the poor and treating the sick when not rushing off to battle nasties like the necromancer, amoral thieves who just look to make a quick coin clipping purses in the market, well-meaning but ruthless knights who seek to put down the aforementioned thieves without realizing their oppressive lords have beggared the people, and a cult to a god of chaos and magic whose followers Blue and Orange Morality pushes them to do things no one understands. Really, the limitation is the player's and GM's imagination and their willingness (or not) to have certain things in their game. They may even be in the same Adventure Town. Newer, more "mature" games often aim at the more limiting Gray and Gray or Gray and Black morality.
Planescape may most exemplify this. You could be a divine servant from a fantasy version of Dante's Purgatorio, a Snark Knight anti-hero out of fantasy Charles Dickens, or a monster from a Milton-like hell. The various groups in the game are all over the map on their ethical stance.
Most Changelings are Seelie dominant and generally good, but not necessarily supremely virtuous. Most Unseelie fae are still decent folks. Some Seelie and a few Unseelie are so old-school knightly they might as well be D&D paladins. Seelie and Unseelie villains alike range from operatic Harmless Villain to ruthless Pragmatic Villainy to cannibalistic Blood Knights to Eldritch Abomination-worshipers.
Mages as individuals are usually trying to achieve good ends. The main conflict is Romanticism Versus Enlightenment, with the Romantic Traditions embracing old school mysticism and trying to awaken humanity and the Enlightened Technocratic Union trying to empower humanity For Science!. Then there are the Eldritch Abomination-serving Nephandi and the insane-as-all-Hell Reality Warper Marauders. The conflict started with the Traditions clearly being morally superior to the Technocrats, but the Technocracy got a little Character Development later on and it became very hard to say either side was right. Individual mages in each group were all over the map, while the Marauders are very much Blue and Orange Morality and the Nephandi are a faction serving evil masters.
Because it's a game by Obsidian (formerly Black Isle), it should come as no surprise that Knights of the Old Republic 2 features this trope pretty significantly. If the player should choose to be Light Side, then s/he and his/her group are fairly close to the Hero extreme. A little further away from the good end, but hard to say by how much, would be the Jedi Council, who are shown to have good intentions but be seriously flawed in their execution of them. Further toward the Villain side, you would have Darth Traya. Then, practically sitting on the Villain extreme, you have Darth Sion and Darth Nihilus, with the second one the most non-Heroic, most Villainous person in the game.
Kingdom Hearts, particularly in its later instalments, is surprisingly dependent on this trope for a Disney property. Sora's pretty close to the hero extreme (though he's more personally-motivated than he seems), while the Disney villains actually come from 'verses with Black and White Morality. The grey areas range from Roxas (whose lack of memories sometimes leads to a sense of Ambiguous Innocence) and Riku and Axel (who are so devoted to their friends that they'll shoot whatever dogs are necessary to save them) to DiZ (who works for the same end as the good guys out of a need for revenge) and Organization XIII (which, in itself, has everything from the apathetic Demyx to the Evil Overlord Xemnas).
While the first Mass Effect had this to an extent, the second game features it a lot.
And at the bottom are the Reapers, who plan to assimilate everyone useful and kill the rest.
Don't forget the Blue and Orange Morality of different cultures, most obviously the geth. For this reason, Legion's loyalty mission has one of the most contentious choices in the game.
The Geneforge series. There are anywhere from two to five factions the player can join in each game. With the possible exception of 2's Barzites and 5's Taygen, they pretty much all have arguments in their favor. While the world itself is more about Gray and Grey Morality, the individual sides play out this trope. The Well-Intentioned Extremist tends to be the most common type in each, but they all have their share of saints and monsters, and everything in between.
Dragon Age: Origins has shades of this. The only wholly villainous faction are the Darkspawn and even they become more sympathetic in Awakening. Dragon Age II takes it even further to the point that there is no Big Bad responsible for everything going wrong. Every major faction in the game is sympathetic to some degree and all of them are partially responsible for the Downer Ending. The games do have a few truly heroic and truly monstrous people, but they have surprisingly little impact on the setting as a whole
Star Wars: The Old Republic is shaping up to be an example of this. From what we know so far, it's just as possible to play a Light sided Sith as it is to play a dark sided Jedi, and a number of characters on both sides are morally grey.
However, let it be known that "Light Side" and "Dark Side" are very different concepts for Imperial characters and Republic characters. At worst, a dark sided Republic character will be a Token Evil Teammate, generally they'll be AntiHeroes. On the other side, Light sided Imperials are generally AntiVillains of various degrees, with the best being Type IVs, devoid of villainous actions, but still on the "bad side."
The smuggler (republic) dark-side story ends with you seizing control of a massive interstellar pirate fleet through murder and betrayal, then using the "distraction" of the climactic good-versus-evil battle of the other storylines to loot and then raze most of the starports in the galaxy in an orgy of murder, rape, and pillage. Additionally, the only person to make any kind of attempt at non-murder conflict resolution in the Jedi knight storyline is a Sith officer, who ends up nobly sacrificing himself for morality while the actual player, light side or dark, takes the easy and bloody way out. I'd say they've got the Grey and Grey Morality covered pretty well.
And the goal of one of the Sith lords on Korriban is the fantasy equivalent of curing cancer.
At the top of the spectrum, you have the utterly innocent Noel Vermillion, Wide-Eyed Idealist. Following that there's both Jubei and Rachel Alucard, the most likely candidates for the Big Good of the series. With them are Bang Shishigami and Taokaka, who fight the good fight despite lacking a few brain cells, and Platinum the Trinity/Trinity Glassfield, who has a bit of a Split Personality problem but is otherwise a decent person.
Below that rank are some more sympathetic Anti Villains and some heroes that are a light shade of gray. Hakumen has his own code of justice and works against the NOL, but his Knight Templar streak makes him believe the only way to save the world is to cleanse the world "in the fires of destruction". Carl Clover used to be a ruthless vigilante, but Character Development made him more sympathetic and pushed him into the ranks of the heroes. Iron Tager and Lambda-11 are pretty decent people who just so happen to work for the rather sleazy Kokonoe, Makoto Nanaya is pretty much a hero, but she tends to be a bit overprotective of her friends, works for the Kokonoe while being a Reverse Mole and implies that she'll backstab pretty much any allies who dares harm her friends. Litchi Faye-Ling is a kind hearted woman who was Forced Into Evil, and Tsubaki Yayoi is a good person underneath the brainwashing.
In the middle of the spectrum, we have Ragna the Bloodedge— The Hero— who is a Jerk with a Heart of Gold at best; his one-man crusade against the NOL was undertaken for selfish ends and he has no hesitation when it comes to killing anyone in his way. Despite becoming a good guy after Continuum Shift, Jin Kisaragi is still an Anti-Hero on the same level as his brother, as making a Heel-Face Turn doesn't stop him from being a titanic Jerkass. Nu-13 is unconcerned with anything else except Ragna... and would kill anyone who gets between them. Arakune is a mindless beast driven by hunger, and his human self Lotte Carmine was a self-serving glory hound.
City of Heroes has Praetoria, which was assumed at first to be a standard Mirror Universe. Then we find out in Going Rogue that Praetoria is actually very much this. The members of the Resistance and Loyalists alike are scattered all across the morality spectrum.
World of Warcraft: There two main kinds of conflict, roughly corresponding to player-vs.-player and player-vs.-envionment play: The Horde vs. Alliance (PVP) is Grey and Gray Morality, a conflict maintained mainly by jerks and ordinary people failing to see things from the other faction's point of view, and the occasional truly bad apple spoiling everything further for everyone else. For example, some of the humans of the Alliance are appalled at the city of Lordaeron having been transformed into an undead hive with rivers of slime, whereas the Forsaken undead living there could point out that as survivors and rebels against the Lich King's plague of undeath and often former inhabitants of the kingdom, they certainly have a claim to their rebuilt city. (But they're also obsessed with trying to poison everyone else.) The other type of conflict is of both factions against destructive, wholly evil forces like the Lich King's Scourge or the Omnicidal ManiacLegions of Hell of the Burning Legion. (Mind you, the Lich King had a bit of a personality conflict himself, and the Burning Legion's founder was driven by an extreme case of Utopia Justifies the Means.) Some organisations opposing such threats, such as the Argent Dawn/Crusade, are clearly good, whereas the otherwise similar-ish Scarlet Crusade is a pretty much unambiguously evil Knight Templar organisation.
A very good example of a morally grey faction is the Uruk Dominion. Basically, they're a city-state reminiscent of Isengard, which came to be after a Gladiator Revolt. It's the only place in the world where the Uruks, Ly Kan and Reptarri are truly free, and their long-term goal is to free the other members of their oppressed races. But not so fast. They breed vast armies of warriors using breeding facilities, using human women, ones that the Uruks have captured and enslaved themselves.
Comes with the the territory of being based on the Dungeons & Dragons alignment system in The Order of the Stick. You have good characters doing good things because it's the right thing to do, bad people doing bad things for a greater good, and bad people doing bad things for amusement.
Sinfest. Satan is definitely evil, if affably so. God isn't evil but definitely a jerk, his son however is definitely good, the Dragon neutral and Buddha somewhre technically neutral but nice. The mortals are all over the place.
There Will Be Brawl uses this a lot. Farthest towards the "Hero" side would be Luigi and Red, who genuinely want the best for the Mushroom Kingdom and its inhabitants, and work to solve the mysteries in the show without resorting to more extreme methods like Mario or Link. Characters closer to the "Villain" side are people like Wario, who's only out for his own self-interests, then Zelda who forcibly attempts to usurp the Kingdom's power, and finally Kirby at the most extreme, who just likes killing people and sowing fear among the populace.
The Whateley Universe does this in spades. Start with the heroes of Team Kimba. They range from the 'I don't even want to hit people' attitude of Phase to the 'I had to slaughter a hundred bad guys to rescue people' switch of Tennyo to Bladedancer, who killed an ordinary family man in cold blood to prevent a possible Bad Future. The villains are all over the place too. Supervillain Dr. Diabolik is apparently a great father, and his children have said he only does the things he does to advance mankind.
Any online roleplay is prone to this, due to the number of creators. Destine Enormity has a wide variety of good guys and bad guys on both sides. The sides are more divided by the Order Versus Chaos axis than anything else, but even that's an informal OOC distinction.
Worm is full of this. Each faction has their own ups and downs, with the superheroes having sociopaths and glory-seekers among their ranks, the villains having several examples of Justified Criminal, and in one case an unrepentant Neo-Nazi who presided over race crimes gives his life for the sake of the city.
In Avatar The Last Airbender, most of Team Aang is unequivocally good and the most powerful members of the Fire Nation are power-hungry sociopaths, but almost everyone else falls somewhere in between. Ba Sing Se turns out to be a Crapsaccharine World, and the Northern Water Tribe has some pretty sexist moments. The rank-and-file and civilians of the Fire Nation are more often misguided patriots than outright evil. You could make a decent argument that the whole series is a subversion of the Always Chaotic Evil trope.
My Little Pony: Friendship is Magic features characters from all over the moral spectrum, where the absolute majority fall within the grey middle-zone. In the case of the heroes or "good guys" in general, this is usually facilitated by Mr. Vice Guy, and most of the villains are Not Evil, Just Misunderstood. Princess Celestia and King Sombra are two notable exceptions, from different ends of the moral scales.
Goof Troop's cast contains an optimistic Nice Guy who only causes problems by accident, a cynical Nice Guy who is harmless except for a few Beware the Nice Ones moments, a Mama Bear who wants the best for everyone but is ruthless in enforcing it, an High School Hustler who spends half his time going out of his way to help his friends and family and the other half taking them for granted, a Bratty Half-Pint who also shows sympathy when it's needed, and a Jerkass who can also be a Papa Wolf when the situation calls for it. Morality of minor characters are not quite this nuanced, but still cover a range from "completely good" to "outright evil" with many places in between.