In the Nightfall Series both humans and vampires make some morally dubious decisions.
Kurt Vonnegut states in the introduction to Welcome to the Monkey House that this is one of the guiding principles of his work: there are no villains, just people with conflicting interests. His characters don't tend to be heroic either.
In Chung Kuo, there is no really good side; both the Han rulers and the European rebels commit atrocities as the story progresses.
The War between Manticore and Haven in Honor Harrington, with the second Haven revolution in the series resulting in a government led by good people, has become this. Indeed, as this carries on it's lost even much of that, becoming more of a Let's You and Him Fight between good guys.
As of Mission of Honor, the governments of Manticore and Haven realize they were manipulated into their wars, and ally to fight Mesa, which is responsible for their troubles.
Featured very prominently from the second series onward in Warrior Cats. The authors have even gone back to write sympathetic backstories for most of the villains, the most notable being Scourge. Tigerstar and Hawkfrost are also noteworthy because, although they wanted power and did horrible things to get it, they only wanted power because they believed they could do a better job of running the Clans and help keep the forest peaceful (Although Tigerstar's vision for running the Clans was very racist). The villains of the fourth series also consist almost entirely of cats that have been wronged or forgotten and are rising up for revenge. Then for the heroes, we have Brambleclaw, who had the exact same goals as Hawkfrost, and leaned dangerously close to The Dark Side, making Hawkfrost's status as a Manipulative Bastard pretty much the only difference between them. We also have Leafpool and Squirrelflight with their (spoileriffic) lies and betrayal. And then there is Hollyleaf, Lionblaze and Jayfeather, who all seem to be much more dysfunctional than all the other characters.
Pretty much everything Guy Gavriel Kay ever wrote falls under this trope. Exceptions:
And Tigana covers the whole spectrum. You've got the sympathetic and "good" Devin and Dianora, then Alessan, Brandin, and Alberico. In other words, it's more like White and Gray and Darker Gray and Black morality.
Animorphs falls under this tropes in the later books. At first it's a pretty clear cut case of the bad guys (the Yeerks, taking over the planet parasitically) and the good guys (the Animorphs, and by extension the Andalites, who also hate the Yeerks). As time wears on, however, it's revealed that the Andalites' response to the Yeerks infesting the Hork-Bajir homeworld was to release a deadly virus into the atmosphere of the planet, killing nearly all Hork-Bajir on their homeworld. If the Animorphs fail to stop the Yeerk invasion, the Andalites have plans to do exactly the same thing to Earth. As well as that, some of the Yeerks start to be portrayed as true characters, with individual motivations and emotions, instead of just a pack of slugs. Even the Taxxons, giant centipede-like creatures get some of this; they're revealed to be total slaves to their own hunger, literally unable to stop eating as long as there is food around. Then there are the Animorphs themselves; over the course of the books they morph from idealistic kids doing the best they can to a hardened guerilla force with no qualms about sacrificing the new bunch of idealistic kids in the name of winning the war. This seems to have been the point of the series.
The Kommandant's Mistress. The entire book is based on a concentration camp Kommandent and a Jewish inmate, who respectively are not entirely a villain and not entirely a victim.
The Chaos Walking trilogy is all about this. While Mayor Prentiss is a darker shade of gray, Mistress Coyle and the Answer's methods of stopping him (no matter what the cost) can be those of a terrorist or a freedom fighter. This is heightened when the heroes are forced upon the two different sides, while being aware of how much rubbish the whole war is. Also the fact that it's practically a gender battle heightens the uncertainty of the war. In the third book they team up in an alliance against the Spackle, even though the Spackle are the ones that were treated so terribly
The Reynard Cycle draws the very clear distinction that behaving heroically doesn't always directly translate to behaving ethically or morally. It also portrays the majority of its villains as driven by understandable (occasionally even laudable) goals and motivations.
The Star WarsExpanded Universe flies up and down the morality scale Depending on the Writer; most of them have pretty clear bad guys, and with Timothy Zahn most of those bad guys aren't so bad, but his book Outbound Flight fits here. There are a lot of major characters, but they end up falling into one of three categories: Jedi and civilians on Outbound Flight, Chiss and captives, and Darth Sidious's agent. None of those are entirely good or evil. Outbound Flight is led by Jorus C'baoth, an arrogant and domineering Master who believes himself to be the ultimate authority, and whom the others are reluctant to contradict. The main Chiss character is Thrawn, who... well, he's at his most heroic here, but he'sThrawn. Sidious's agent is planning to destroy Outbound Flight, but he doesn't exactly cackle and he respects Thrawn. The few unambiguously good characters have subplots, but in the end all they're able to do is die to save fifty-seven out of the fifty thousand who were on Outbound Flight.
On the one hand DORLA in Kit Whitfield's Benighted uses police state tactics and functionally, if not officially, operates on a "guilty until proven innocent" mentality. On the other hand they do a dirty, dangerous and very necessary job and get less than zero appreciation for it from the public.
There's an interesting variation on this trope in Jack Campbell's Lost Fleet series: the protagonist wakes up from almost a century in suspended animation, having been "killed" in the first battle of a presumably White on Grey war, to find the same war still raging, but with both sides reduced to the lowest possible moral levels as a result of ridiculously high attrition and a circle of atrocity and counter-atrocity. Being understandably appalled at this, he goes on to teach his fleet about honour and efficiency to move it away from Black on Black to Black and Gray Morality before exploring the mindset of his Syndic enemies (upgrading them from Black to merely ridiculously inefficient dark Grey). And then it turns out that there are ineffable aliens (with their own morality altogether) behind it all. By the end of the story, Geary only manages to deal with the aliens by completely defeating the Syndics first and getting to the other side of their territory.
In the A Song of Ice and Fire series and its television adaptation, no one major faction is wholly good or evil — each has its own unique positive and negative traits; it's the methods they choose to use that decides whether they are face or heel:
The Starks are "heroic" because they are honorable to a fault and prefer diplomacy over warfare. Despite this, one of their most useful bannermen is Roose Bolton, who is tolerated as a Token Evil Teammateuntil he finally betrays them, and testimony from peasants in the wrong place at the wrong time show that Stark grunts do Rape, Pillage, and Burn just as much as the Lannisters. Also, while house heir Robb Stark tries to live his life honorably, he is too easily swayed by his passions, openly violating his contracts and tossing aside loyal alliances in order to marry the woman he loved, and allowing his ambition to grow too big. What began as a quest for Northern sovereignty eventually morphed into an all-out war against Southern Westeros, an ambition for which he and his men ultimately paid the price.
The main Baratheon family is a mixed bag, because King Robert is shown as a charismatic ruler who is at least savvy enough to surround himself with able advisers. On the other hand, his son (by his wife Cersei through Brother-Sister Incest with Jaime) Joffrey is psychotic, immature and capricious, with his only redeeming trait being his yearning to win his father's approval.
Renly Baratheon's faction is "heroic" because they fight honorably, have several noble warriors on their side, and are one of the few factions that accepts all regardless of status, including women and homosexuals. That said, they are fools who are still fighting a bloody war for personal honor and glory rather than for a legitimate desire to rule Westeros peacefully.
Stannis Baratheon's faction is "villainous" because they use incredibly creepy Black Magic and assassinations to accomplish their goal which is ultimately noble. This is finally proved when Stannis, at Davos' insistence, finally realizes that if he is a true king it is his duty to protect his subjects by temporarily putting his ambition on hold and going to the Wall. So far, he is the only ruler to actually accept responsibility in this way.
Daenerys Targaryen is "heroic" because she is fighting to reclaim the Iron Throne, despite being constantly reminded that her father, Aerys II, was a lunatic, and that commoners would rather be left alone. She initially believed that the commoners secretly prayed for her return, but even when disabused of this notion she still thinks of wreaking revenge on the "usurpers" instead of considering if Westeros even wants the Targaryens back in the first place. As the story progress she becomes a crusader against slavery and exploitation but conquers whole cities in the effort to eradicate the practice which proves equally problematic. She also shows no remorse for ordering deaths, including burning a woman alive.
Varys is "villainous" because he is one of the top chessmasters of the brutal civil war, who did as much as anyone to bring it about, but his claim that he genuinely cares for the realm makes him more sympathetic to some readers, especially as compared to his intellectual rival, Petyr "Littlefinger" Baelish, who is an outright sociopath. On the other hand, certain of his actions make it clear he's only interested in stability on his own terms, as seen when he kills Kevan Lannister when he was starting to pull King's Landing back together after Cersei's reckless craziness.
Kevin J. Anderson's Terra Incognita series. Examples ranging the spectrum from the very good to the very evil can be found among both the Aidenists and the Urecari while the Saedrans stay strictly neutral.
Daniel Suarez' Daemon series, or more specifically the 2nd book of the Duology Freedom™. While one side is depicted as evil from the beginning of the first novel that notion gradually changes throughout throughout the novel. Furthermore iconic characters of the novel show sympathy, respect and even adoration of key members of their opposing side.
The Old Man's War series: The Colonial Union really wants to protect and preserve the human race in a universe full of hostile aliens who want to eat them. But they're basically a military junta using some questionable, authoritarian methods: recruiting the majority of their soldiers from a planet (Earth) kept completely in the dark about the rest of the universe, and vat-growing a group of emotionally-stunted, effectively Child Soldiersfrom the bodies of the dead as Special Forces, restricting civilians from certain technological advances, and engaging in aggressively expansionist wars of colonization, steadily turning the rest of the galaxy against them. On the other side, there actually are many hostile alien races who want to eat humanity, but most end up joining the Conclave out of a desire to use diplomacy to try and minimize aggressive war and further bloodshed.
The three empires in the Quintara Marathon series demonstrate this, at least in terms of the humans who are represented in all three. The Exchange is a free-market free-for-all with the most personal freedom, but minimal social safety nets and an underbelly of corruption and unofficial slavery (in the form of genetically engineered intelligent beings considered as property). The Mizlaplan control a rigid theocracy where they are unquestionably the rulers (and effective gods), inquisitors and priest can use whatever methods they feel are necessary, sexual discrimination against women is part of the system, and where brainwashing into absolute obedience is commonly used, but where most people live peaceful, safe lives without concern about going hungry, crime, or actually being personally oppressed. The Mychol Empire is a dog-eat-dog vicious society with oppression, slavery, and a great deal of violence, but where everyone has the opportunity to rise if they are smart enough.
In Lonely Werewolf Girl no one is really heroic; Kalix killed her father, Sarapen is batshit insane, the rest of the werewolves downright callous and manipulative, Moonglow cheats on her boyfriend, Daniel is trying to be a Dogged Nice Guy to Moonglow, Malveria a Retired Monster, and the Avenaris Guild of werewolf hunters are trigger happy sociopaths.
The Civil War in Bernard Cornwell's Starbuck Chronicles. This is because rather than deal with the causes of the war he approaches it from the perspective of the individuals on both sides and finds that there are heroes and scoundrels on both sides. Emphasized by making the viewpoint character, Nathaniel Starbuck, a "Copperhead" (a Northerner who sided with the South) and another major character, Adam Falconer, a "Scalawag" (a Southerner who sided with the North).
Gone, by Michael Grant. All the characters are kids under the age of 15 who are trapped in a bubble without adults. On their 15th birthdays, they disappear, too. That's called the "Poof". The heroes are trying to figure things out, put things back to normal, learn how to use their new powers, and figure out how to survive their 15th birthdays. The villains have mostly the same motivations, except that their methods are different. The heroes sometimes do bad things, and the villains sometimes do good things. Basically, they all just want to survive. The exception is Drake, who Michael Grant has confirmed is pure evil, no shades of gray. Penny is also wholly evil.
Fugue for a Darkening Island invokes this trope, 70's Britain split into civil war as thousands of African refugees flee into Europe to escape a nuclear war. The refugees are innocent and desperate, but often violent and thuggish. The fascist government is cruel and oppressive, but the only thing preventing the total collapse of the country. The secessionist movement is liberal and free, but weak and elitist.'
Paolo Bacigalupi's The Windup Girl is very dark grey on all sides. The calorie men are out to make profits by whatever means necessary, but they're also trying to stave off unending waves of plagues and blights. The Kingdom of Thailand heroically resists the outsiders who want to plunder it, but it's also deeply corrupt and politically unstable. Hock Seng, who appears ready to do anything to save himself, also has one of the most depressing backstories, and when we last see him, he is risking his own life to save a little girl. A character who looks heroic will turn out to have something very dark in their past (or present), while one who looks villainous may have honorable intentions.
David Drake's Hammer's Slammers does a good job of showing how this trope appliesinwar; both the titular mercenaries and their opponents do some prettydespicable things in order to hold their own losses down, like nuking a rebel stronghold because attacking it any other way would result in unacceptable losses for the attackers. When the series deviates from Gray and Gray, it's usually to go to Black and Gray, especially if MajorJoachim Steuben is involved.
Keys to the Kingdom has a lot of this as well. Dame Primus is quite The Chessmaster, and not in a good way. The only truly good character is Arthur, and he barely has any idea what's going on for a lot of the time.
In The Kingdoms of Evil: The main character is put in charge of all the evil in the world. Next up, figure out what the hell evil actually is.
Jodi Picoult's My Sister's Keeper. On the one hand, we have a mother who is desperate to save her daughter's life, even if it means subjecting her other daughter to a variety of increasingly invasive medical procedures against her will. On the other hand, we have a girl who doesn't want to undergo dangerous and painful medical procedures anymore and wants to be seen for herself rather than as replacement body parts for her sister, even if it means taking away her sick sister's last chance at survival. Welcome to the world of no right answers, folks.
Summarised perfectly in this quote from Anna:
Anna: Even if we win, we don't.
Jodi Picoult, period. "No right answers" is pretty much her stock in trade...
The first book of the Artemis Fowl series has this in spades. Artemis freely admits that he's a greedy, manipulative villain, but he aims to use the gold from his kidnapping/extortion scheme to find his lost father and his mother is millimeters away from a nervous breakdown. The LEP just want their officer back without paying any gold, but they go through some very dark means to get it and even intend to kill Artemis if none of their other plans succeed.
The soldiers and rebels in Beachwalker are both portrayed as having sympathetic members, and the book entirely avoids taking sides in their conflict, focusing instead on the specific combatants and civilians in the protagonist's immediate sphere of influence.
The Black Company by Glen Cook at best. Most prevalent in the first book, and then appearing here and there throughout the series.
The people on either side of the diamond wall in Dirge for Prester John view themselves as the real Pentexore. Neither side is more valid than the other, just one side has the benefit of the Fountain of Youth.
All sides in The First Law trilogy have a mix of good, evil, and indifferent. Then groups of good guys from a mostly evil faction will have a Token Evil Teammate. Then that evil guy might have a good side. It is a mess where an avowedly morally indifferent protagonist character from a corrupt faction of the nominal good guys recognizes that someone's treason was probably the morally correct decision while still pursuing his country's aims. Another book follows a war with protagonist characters on both sides.
In Michael Moorcock's book; The Eternal Champion, the humans are seen as good for the first approximate fifth of the book, but as the story progresses the humans are switched to being about on par with the Eldren (Humanity's inhuman enemies), and towards the end, even Ambiguously Evil.
Gone Girl: No character is completely good or completely bad. For example, Margo is a nice character for the most part, but she does flick off the police and doesn't seem too upset by Amy's disappearance. Tanner Bolt wants to help Nick, but he only really cares about winning the case and not about Nick's safety. Desi seems to mean well, but he is, at best, a Well-Intentioned Extremist. As for Nick, even though he didn't actually murder his wife, he's still a dick. He cheated on her, he used her, and he openly admits at one point that he was kind of relieved when his wife wasn't at home. As for Amy, despite having some serious mental problems and doing a lot of horrible things, it's implied that her parent's 'Amazing Amy' books and their insistence that Amy should always be perfect led to her eventual Sanity Slippage. In fact, the closest thing this story has to a purely good character is Noelle Hawthorne, but she's a pretty minor character.
Black Crown: Depending on your views about the conflict in 'Schism', either side could easily be seen as a reasonable way to deal with the situation. May become A Lighter Shade of Grey for whichever side you take.
In The Dresden Files, aside from Harry and his friends, a large number of groups aren't quite so cut and dried.:
The White Council, portrayed as axe-crazy templars in the first few books (due to picking on Harry personally), are later shown to not only genuinely be serving their greater good, but that that good is actually the best of a lot of bad options.
The fae courts are more Blue and Orange Morality than black and white to begin with, but the almost-human members and even many fae seem to have the same mix of malice and innocence as vanilla mortals.
Gentleman Johnny Marcone is a gangster of the Al Capone school, and thinks nothing of murder to protect his business interests... but he hates inefficiency with a passion and prevents more "unnecessary" murder than the entire police force put together, as well as suppressing rivals' crime on his turf. There have been hints that the police aren't so much afraid to go after him as that they simply don't want to, as his way is preferable to disorganized crime.
Harry himself has slipped off of the slippery slope more than enough times to qualify as more gray than white, though in his case it's at least not typically willingly— something that the people on his side regularly assure him still puts him firmly on the side of right, and everyone else isn't so sure of.
This is a major element of The Truth About Celia Frost. Dr. Hudson even lampshades this:
Celia: I understand the difference between right and wrong, and what you've done is wrong!
Dr. Hudson: You're being naïve. Wouldn't it be simple if everything was really as you see it? Black and white, right and wrong. But I'm afraid life is more complicated than that. Those messy grey areas keep getting in the way.
The Mirrorworld Series: Kami'en and the Goyl versus Empress Therese and the Imperials. The Goyl seem like the logical villains until you find out more about Therese's ruthless tactics. Not to mention, their hatred of humans is a natural response to years of human aggression. Then again, Therese and Austrya aren't entirely unsympathetic either...
The Nexus Series: Multiple factions come into conflict over how to use the titular Nexus 5, which allows a user to have a permanent and unobtrusive Brain–Computer Interface. The developers of said technology just want to see how many cool things they can do with it, believing the benefits outweigh the risks. As soon as the technology becomes available however, terrorists and criminals begin using it to create slaves and suicide bombers. At the same time, parents of autistics use Nexus to communicate with their afflicted children and help them socialize. People using Nexus start to resent being subjugated by the anti-transhuman laws designed to protect the rest of the populace, and some are driven to become exactly the monsters that the laws were drafted to fight. With very few exeptions, it's pretty hard to write one side or the other off as being completely in the wrong.
Kindling Ashes: Each side believes that this is a case of Black and White Morality but the dual protagonist system shows that each side has grievances. One dragon recalls how humans killed his mate, broke his Flyer, and smashed eggs, while in the next chapter, that human recalls how that same dragon teared down towers and burned humans alive.
In Czech fantasy/horror series Hammer On Wizard (roughly translated as Kladivo Na Čaroděje) is second to none line between good and evil. Almost everyone there is motivated either by money, career, saving his/her sorry butt or some personal reasons better left unknown. Living in Crapsack World, where No Good Deed Goes Unpunished plays a role too.
In Dark Ones Mistress the MC Clarabelle learns that the ruler of her kingdom (the Dark One of the title) uses criminals in the royal army, keeping them leashed by way of stealing their souls. Innocent people sometimes get caught in this web and while killing him off is the only way to free them, it would basically unleash hell on the populace.
Daniel Abraham's The Dragon's Path, book one of The Dagger and the Coin series, has, as one of its most sympathetic, likable, and humane characters, a mass murderer who burned down an entire city, killing thousands of innocent civilians, out of pride. One of the main conflicts is between two factions of aristocrats, one of which wants to liberalize the empire, allowing greater representation within government to the common people, but which is willing to use assassination and treason to accomplish its ends, and the other, which is trying to maintain the privileges and powers of the aristocracy, but is more honorable and patriotic.
Bear in mind, however, that subsequent books in the series become less grey, as the guy who burned down the city in book one becomes a lot less sympathetic. He has Jumped Off The Slippery Slope by book three at the latest, and may even have passed the Moral Event Horizon by book four.
In Penryn and the End of Days, Penryn falls back on quite harsh, if desperate measures, to get to Paige, like brute force and blackmail. Many humans live as gangs, terrorizing, mugging, and killing others and trading with parts of angels. Others live as servants and courtesans to the angels. Most of the angels, however brutal and dangerous, don't even know why they were sent to Earth. That the humans shot their leader might be a motivation for their cruelty as well.
In Hullo Russia Goodbye England, the pilots who are Britain's frontline nuclear strike force strive to suppress the unfortunate truth that in defending Britain by nuking Russia and killing millions of people, they're proving themselves no better than the despised communists opposite.
The war between the Hominum Empire and the orcs in The Summoner Trilogy is this. While the orcs may be Always Chaotic Evil who have long preyed on the humans, the Hominum Empire escalated the conflict by invading and clearing the orcs’ forests to fuel their industrial revolution, dragging the two races into a nearly-decade-long war with casualties so high, the humans have resorted to using Child Soldiers and conscripting prisoners.
The conflict between the humans and the dwarves, as well. The humans have conquered and oppressed the dwarves for centuries, but the king has said he'd be glad to loosen the restrictions placed on the dwarves if they'd stop trying to rebel and kill his people.
In The King Beyond the Gate Ananais, the whitest morally of the three protagonists, has "freed" prisoners ambushed and killed to prevent them joining the enemy again.
The conflict of Dune starts out as an example of Black and White Morality between the prominent Houses of Atreides and Harkonnen (with a little help from the Emperor to tilt the outcome in his favor), but very quickly veers into grey territory once Paul throws his lot in with the Fremen. And that's just the first book. Eventually the series' focus expands to include multiple factions with varying shades of grey who are all more or less just trying to do what they think is best for their own people, as well as the few gifted with prescience who are trying to do what's best for the human species. And then the Honored Matres show up.
Discussed and defied in Carpe Jugulum. Reverend Oats, a pastor from a formerly fire-and-brimstone faith that's undergone massive schisming, reformation, and debate, tells Granny Weatherwax that moral questions have many shades of grey. She scoffs at the idea, as her life has been a grudging understanding that knowing the difference between right and wrong she must always choose right, and that any shades of grey are merely "white that's got grubby."
Wolf Hall, set as it is in the court of Henry VIII, has a lot of this. Thomas Cromwell comes off as the most sympathetic character because he's the protagonist and displays many admirable qualities—he's a good father, incredibly loyal to Cardinal Wolsey, and for most of the story has a genuine admiration for Henry, but as Henry becomes increasingly volatile, Cromwell follows his orders not only to keep his own head but to exact revenge on his enemies. Thomas More is presented as The Fundamentalist who unapologetically tortures and burns heretics, but who is willing to die on the block for his own faith. Anne Boleyn, though often unpleasant, is nonetheless to be pitied as she's led to the scaffold. The Tudor court was not a pleasant place to live.
In The Witchlands, most people aren't truly evil or completely good. Most of them are simply trying to protect their families and their countries, leading to conflicts of interests.
In Alexey Vinokurov's The Country of Three Lands there is a subversion of White, Grey and Black morality, as the titular three lands are actually called White (for the good guys), Grey (for the in-between fraction), and Black (for Chaotic Evil). However, the White Land practices Fantastic Racism and its rulers are Weak-Willed enough to betray the main characters for their city's safety; the Black one, while its king does live up to his Big Bad title, has many morally gray guys.
Dreamblood Duology: Whether Gujaareh or Kisua can actually be called morally superior to the other is a constant question in the books, and one that ultimately goes unanswered. Gujaareh's rulers actively deceive their citizens, but Gujaareh has known years and years of peace, while Kisuati enjoy more freedom in a notoriously unstable country and generally look down on anyone not Kisuati for not following in their footsteps.