In J. R. R. Tolkien's universe, two of the Valar (demi-gods that run the world), Mandos, the lord of fate and the halls of the dead, and Nienna, the lady of pity and remorse, who always wears grey and lives out on the edge of the world, are both benevolent entities. When the sun and moon were created, a third Vala, Este, the lady of rest, asked that the sun not always illuminate the Earth, and that there be a period of darkness every day so that creatures could sleep. The Elves themselves first came into existence during a period before the creation of the sun and moon, and so Elves revere the night sky and love the stars above all other sources of light, many of them were unwilling to leave their homeland to go to the Home of the valar, the land of light, and so are called Dark Elves, but they are not evil.
The titular character of the Skulduggery Pleasant series is a walking, talking skeleton who wears black suits, drives a vintage black car, and has no problem whatsoever with brutally killing his enemies, especially where it's revenge for his murdered family. Despite all this, he is most definitely the good guy.
In the later books, Valkyrie is revealed to be the "Dark Messiah," Darquesse and begins using necromancy, but for good reasons. Whether or not she'll stay not-evil remains to be seen.
In the novel Dead Beat, Harry talks with Kumori, a powerful necromancer who uses her powers over life and death to preserve life wherever possible, and is confronted with a deep, unsettling realization that the powers of necromancy, classified as Black Magic by the White Council and considered pure evil, can be used for good ends (for example, keeping a man dying of a gunshot wound alive by simply refusing to allow him to die at all). At the end of the book, Harry puts this into practice, when he reanimates a Sue, the T. Rex skeleton at the Field Museum, and uses her as his mount to save the damn day.
Later, in Changes, when talking to his godmother after Susan is killed, the Leanansidhe, a powerful fae of the Winter Court (which is considered the cruelest and most wicked of the faerie courts) states that she will bury her as Harry wishes her to be, at no cost to him. This prompts Harry to remark that just because Winter is cold, it isn't always bitter.
Further on, in Ghost Story, he encounters an angel of death watching over Father Forthill when he is close to death. Every physical aspect of the angel is black with the exception of her irises and sword. Despite all this, she has an innocent personality and is simply there to guard Forthill's soul in the case that he does die, from whatever horrors lurk in the spirit world, including the Prince of Darkness would love to capture this good soul.
Also, in Cold Days, we find that the Winter Court has a very vital purpose. They are constantly fighting a war against the Outsiders, at the Outer Gates to preserve the world.
The Genius Loci known as Demonreach isn't evil. In fact, it is the warden of a prison designed to keep various evil entities, the least of which are demi-gods, away from humanity. This doesn't prevent it from being surly, anti-social and and having little use for interaction with anyone.
Well, of course it's anti-social. It is a prison, keeping a lot of very dangerous demi-gods and gods imprisoned. It doesn't want any outsiders showing up poking around trying to stage a prison break.
Black Magic in Labyrinths of Echo by Max Frei only differs from its White counterpart in that it deals with material substances and not etherial. High-level Black spells are used... in cookery to create exquisite cakes.
The Professors of Light and Darkness are not enemies, merely friendly rivals, and each is a harmless, basically likeable character in his own way. In fact, the titles are actually designations of what they study; the Professor of Light studies the mysteries of illumination, and the Professor of Darkness studies the mysteries of light's absence.
Less literally, the slaughterers. They're nocturnal, look like blood-red goblins, and have a sinister-sounding name. They're actually peaceful and relatively friendly, and they get their name because they slaughter in the true sense of the word — killing and butchering animals. In fact, their work is why they're red from head to toe- apparently, the chemicals involved in their tanning and spicing (or possibly sympathetic magic; there's stranger things in the Edgewoods) permanently stains their skin and dyes their hair. Unfortunately, despite this, they're undeservedly reviled because of their strange appearance and distasteful work. This is highlighted by the fact they are the most peaceful and welcoming of the races that Twig, protagonist of the first published novel, meets; he actually gives serious thought to staying there until the Gloamglozer tricks him into leaving, and later stories reveal he eventually returns to them and marries a slaughterer girl.
The Overlords in Arthur C. Clarke's Childhood's End aren't evil even though they looked like demons.
The Tiste Andii are the Children of Darkness, humanoids with black skin and darkness-themed powers. But they are no more evil than any other people in that world, and seem better than their cousins the Tiste Liosan, Children of Light, who are bigoted Knights Templar.
Oh, and by the way, the lord of the Tiste Andii is ultra-badassAnti-Villain Anomander Rake (Knight of High House Dark, Son of Darkness, etc).
Trolls? Though they're very blunt and traditionally not fond of humans and dwarfs, they're as capable of nobility and generosity as other races and generally portrayed sympathetically. Created largely as a reaction to the implication in Tolkien that big, scary-looking humanoids were Always Chaotic Evil.
Several witches, including Granny Weatherwax and Miss Treason, who cultivate a sinister, Deadpan Snarker attitude but generally mean well.
Most of the undead are entirely harmless. Reg Shoe, Maladicta and Otto Chriek spring to mind in particular. It's true that Discworld vampires are instinctively predators, but many are trying very hard (and with relative success) to become useful, productive, and nonthreatening members of society by turning their fixations to other obsessions, such as coffee or photography.
And even the traditional ones aren't always pure evil, provided they know where to draw the line, such as the Count Bela de magpyr from CarpeJugulum, who unlike his nephew doesn't seek to dominate anything much, and in fact has developed a certain rapport with the local townsfolk, which may be mutually beneficial.
Death is one of the kindest and most compassionate entities in the Disc, having always stood up for life against its enemies.
Lord Havelock Vetinari is a ruthless despot who keeps the city of Ankh-Morpork tamed and functional through sheer force of will and a terrifying intellect. But his goal is to make the city a better place for everyone (except mimes), and he's been resoundingly successful - he has no personal ambitions himself. If anything, he seems to be methodically preparing Ankh-Morpork to run itself when he retires or dies. He has built up a reasonable Watch, rebuilt the post office, helped introduce paper money and encouraged a lot of other races to immigrate, increasing the city's prosperity.
This is represented well by Vimes and Carcer in Night Watch. Carcer is a garrulous, smiley, talkative chap who is able to charm even Vimes, to a degree. Vimes, on the other hand is a Jerk with a Heart of Gold, a crowning example of Good Is Not Nice, and sports an eyepatch and a nasty facial injury. Carcer is an unrepentant murderer, while Vimes is a quasi-mythical force for justice, who only wants to protect the innocent.
In fact, in Thud! it's revealed that Vimes has an inner watchman, the "Guarding Darkness", which keeps the darkness inside of him. Including a literal demon. When Vimes says that he's the watchman who watches the watchmen, and that's including himself, he isn't kidding.
Dwarven philosophy is chock-full of this. Humans are "enlightened" because they live in the blinding sunshine, Dwarves are "endarkened" and live in the caves, where the eyes are not blinded, but must open as far as they can.
Although they often serve morally unconventional people, the hideous (females excepted) Igors are generally quite pleasant and humanitarian, having become a lifesaving fixture of the medical industry wherever they go. Their Code actively prohibits them not taking steps to save a life (with exceptions if they've been mistreated), and almost every Igor introduced as a character has been likable, well-intentioned and eager to please. In Uberwald at least, Igors are considered quite the eligible bachelors, and Igorinas are always stunning. (Given their obsession with self-improvement and body-part transplants, most people have come to certain... realisations.)
A recent addition to the faculty of Unseen University is Dr. John Hix, the head of "Post Mortem Communications." Which is notNecromancy at all, obviously, because Necromancy is illegal and Post Mortem Communications is not. Hix lives and breathes by this trope, making a conspicuous point of wearing black and showing everyone his very gothy skull ring, as it is apparently his job to do "evil", but only within "acceptable limits", a token dark magician. Hix isn't really evil at all, as the worst of his acts involve the occasional blunt remark that no one else would say aloud because it would be impolite. Though he does slip tickets to his theatre troupe's performances. And being the head of legal PMC means he can very legally take care of those illegally practicing Necromancy. With fireballs.
Black magic is order magic, while white magic is chaos magic. The reason given is that black is the absence of color and thus represents complete order and white is all colors squashed together and therefore chaotic. Of course, chaos magic isn't necessarily evil either. Just destructive. (Still, the fact that "Angels of darkness" and "Demons of light" are common expressions shows that many perceive darkness as better than light in this universe.)
In the first book of the saga, black magic is pretty unambiguously good (albeit overly rigid) and white fairly unambigiously bad, with the ostensible "banishing" of Recluse malcontents played as an attempt to spread the benefits of order to the less civilized continent that neighbors the island nation and educate black wizards in the responsible use of their power. It's only after three or four books that we're even introduced to a sympathetic "white" magician, and even then they're only "good" because they go against their evil culture of ultimate evilness and at least partially embrace black magic. Pure black magicians are never presented as unambiguously evil in the same manner as pure white ones, though the grey wizards are still the obvious mary sues of the series.
The book takes this farther, adopting as a major theme that "most demons weren't deep down evil. In the great cosmic game they felt they occupied the same position as tax inspectors — doing an unpopular job, maybe, but essential to the overall operation of the whole thing." These are actual from-hell fallen-angel straight-out-of-the-new-testament demons, but they're not really evil.
Hey, Crowley "did not so much fall as saunter vaguely downwards."
The Nights Watch is completely dressed in black, but is one of the most honorable societies in the whole universe. Well at least the part that doesn't consist of former criminals. Although they are pretty honorable. The Watch has been running on rapists, murderers, and traitors for a long time. They still do their duty.
The common criminals, bastards, and other dredges of society protect the realm while the best knights in Westeros, the Kingsguard, wear white and may end up destroying the realm on the orders of an unfit king.
And in contrast, Bloodraven says that darkness is a source of strength and protection for greenseers. This may turn out to be a subversion though, what with the old gods' history of receiving human sacrifice.
Jacqueline Carey's The Sundering, whose original title was Elegy for Darkness. In it, the "dark god" Satoris is dark because he has been burned and constructs his dark fortress as protection. He protects the outcast and the despised, and answers the prayers of those who honor him. His minions are honorable and thoughtful creatures, who only fight to defend themselves. It is the armies of the Light that engage in genocide (forbidding defeated species from having babies) - and should they win, humans might stop having babies too.
Stephen Baxter's The Time Ships, a sequel to the HG Wells The Time Machine, sends the Time-Traveler into a very different future where he is rescued from an inhospitable far-future Earth by a more civilized version of the Morlocks. The Morlock who becomes his sidekick has to spend quite a lot of time convincing him that the Morlock tendency to skulk in dark places is not evidence of an inherently evil nature (in fact, he implies that they chose to live in the dark to improve their night-vision for stargazing). It comes as quite a shock to the Victorian Time-Traveler to realize that his distate for Morlock appearance and habits has more to do with his own body issues than with some kind of inherent evil in the Morlocks.
Soulcutter from Fred Saberhagen's Third Book of Swords might count. Unlike the other Twelve, its hilt has no symbol, but is rather all black, and even its blade is dull. And its ability might seem evil, as it imposes a crushing despair on everyone within its area of effect; for this, it is nicknamed the Tyrant's Blade. For all that, though, the one time we see it used, it is to stop the evil would-be world-conqueror Vilkata.
On the other hand, Vilkata is also known as the Dark King, so that would certainly be an inversion of this trope.
The Black Elfstone in Terry Brooks Shannara books is not evil, although its magic can certainly be put to destructive purposes. It's only black though because its power is to absorb magic, just as black objects absorb light.
The power of the Druids is stated to be of the same origins as the power of the Warlock Lord, and the power of the Sword of Leah comes from immersing the sword in the dark afterlife pool that is the Hadeshorn.
Allanon from the Sword Of Shannara series appears at first as a secretive and intimidating seven-foot tall man dressed in black robes. Later, he is seen communicating with the dead and utilizing frightening magic. However, he is unquestionably on the side of the protagonists.
In Curse of the Mistwraith and its sequels, Arithon controls the powers of shadow, but he's a pretty nice guy. His half-brother, Lysaer, controls the powers of light, but due to the titular curse he's a bit of a douche. His biting manner is actually a mask for the fact that he has no choice but to empathise with every living creature's pain.
In Anne Bishop's Black Jewels Universe, three main, sympathetic and hot characters are named Saetan, Lucivar and Daemon. "Dark" simply means "more powerful", and does not carry any connotations of evil.
In the Perry Rhodan Universe, the Solar Empire once got into conflict with an alien race over an artifact. They looked like stereotypically devils (which caused the plan to let them meet some Earth Kids for evoking sympathy gloriously backfire), but were shown trying hard to understand Humans (which was difficult due to a very different way their brains worked) and resolve the crisis diplomatically.
Diran Bastiaan, the protagonist of The Blade of the Flame series, is a former assassin who dresses completely in black, has black hair, and is generally creepy in appearance. He is also a pious priest of one of the main forces of good in the world and has all of the good traits generally associated with his church with none of the extremist qualities that kill its reputation in most of the world.
Ursula K. Le Guin's The Left Hand of Darkness: There are two main religions on the planet, one of which, the Handarrata (the other is actually a cult that kind-of broke off from them, but they don't share this belief), see Darkness as equally important and good as Light, as evidenced by the first two lines of one of their texts, from which the title comes:
Light is the left hand of Darkness, and Darkness the right hand of Light...
In David Eddings' Tamuli trilogy the Delphae are cursed by their own god with bodies that shine light and a touch that can melt a man. Despite all the connotations of the word "curse", this change is ultimately beneficial to the Delphae once they can control it. Further, the difference between "blessing" and "curse" is one of definition. A blessing is noticable and "shimmers in the air" while a curse is "dark and silent" and undetected.
The most recent Redwall book speaks of a "dark beast" throughout the entire narrative. It's a black otter out to wipe out the Raven Big Bad, who is an obvious subversion of this trope.
Severus Snape. He dresses in black and looks like a stereotypical villain (and he is vengeful, petty and openly biased to boot), he saves Harry's life on more than one occasion, and in the end puts himself at incredible risk and ends up being murdered in order to help out the protagonists.
Also from Harry Potter, thestrals look like black, skeletally thin horses with "dragonlike" faces, leather wings, blank white eyes and wild black manes and can only be seen by those who have witnessed death and are thus considered creatures of ill omen, but prove very useful to Harry and his friends in OotP and fight in defense of Hogwarts in the final battle in DH.
Sirius Black, Suspected mass murderer, crazy escaped prisoner and death omen lookalike?!
The movie adaptations probably stress this further, as Hogwarts itself seems gloomy and dark at times. Worth to note is also the fanfic My Immortal, which tries to invoke this trope but, as in everything it builds itself up to be, fails horribly.
Hagrid seems to be of the opinion that, when it comes to magical creature, Dark Is NEVER Evil. Whether the creature in question is a thirty foot tall vicious three headed dog, a firebreathing dragon, a spiked, fire spewing snail, or a monstrous spider, Hagrid always believes that deep down every one of these creatures is good and pure. As a result of these, he regularly puts Harry and friends at risk by accident, such as when he sent Harry and Ron into the forest alone to confront a carnivorous and not good-at-all (except towards Hagrid) giant spider. If it weren't for the sudden arrival of Ron's father's old car, which is now borderline feral and living in the woods, Harry and Ron would've died.
And Harry himself. Who would expect Voldemort's Parseltongue-speaking Soul Jar to be the hero of the story?
Specter and Shade from the Seekers of Truth dress all in black, and they use the darkness itself for their abilities. And they're good guys. Not exactly warm and fuzzy, but good nonetheless. The Wizard also wears all black, but more for style in his case.
Ghouls and Nightgaunts that inhabit the Underworld in H.P. Lovecraft's Dreamlands are a far cry from pure evil, and compared to the monsters inhabiting the outer voids they are downright cuddly. While they can be dangerous to any unprepared traveller who goes too near to the caves the Nightgaunts are set to guard, they can befriend and give aid to human dreamers. If you don't mind their habit of eating rotting human corpses stolen from the cemetaries of the Waking World, they can be downright amiable lot, once you learn to know them.
In The Silver Chair the Green Witch's minions look like streotypical devils (horns, spiked tails, etc although with grey skin, not red). In the end it turns out they were her slaves and have no desire to invade the upper world because their home is in the warm depths of the earth and the surface world is much too cold for them.
In the film version of The Lion, the Witch, and the Wardrobe, Mr. Beaver suspects the Fox of being one of the White Witch's spies because he looks similar to his wolf relatives. The Fox of course is their ally and is greatly helpful.
Taken further in the movie adaption of Prince Caspian, where the Minotaur's (all dark furred and intimidating looking) are fighting against an evil king. The Pevensie children even mistook some for villains when they first saw them after getting back to Narnia.
Raymond E. Feist's Riftwars books have the Epic Wizard Macros and later Pug, who's nothing short of a champion of the forces of good, has the title "The Black".
Daemons. True, they are NOT connected to Christianity's demons, but they seem to be strongly based on the daemons from the Greek Mythology (dark spirits that were later demonized by christians), and they are meant to represent consciousness, being partially responsible for free will, something that that Christianity (well, at least the medieval catholic church in Lyra's world) is obviously against. Thus, by representing that "undesired side" of mankind, they represent our dark side. In addition to daemons, most fallen angels (such as Balthamos and Baruch), which are good, are only visible in poor light conditions.
The Harpies count as well. They are described as having a monstrous appearance and at first torment the souls of the dead. But later it's revealed they were just bored and didn't know that they could do anything else. The Protagonist makes a deal that if the dead tell the harpies stories then the harpies will escort the dead through the afterlife.
The Erdlings from Zlipha Keatley Snyder's Green Sky. They have darker skin (the areas where they gather food are not shaded by grund-trees), wear furs, eat meat, and accept the occasional bad seed as a reality with means to deal with it (though they still are Space Amish by our standards). Contrast with the Kindar who live in the trees, wear silks, have a Veganopia, and have banished even the concepts of anger, sorrow, and violence. Guess which society is ruled by the Knight Templar secret society...
Marrow Bones from the Xanth series. He's a talking skeleton, but he's also friendly, laid-back and even-natured. Even though he can never understand how humans find it comfortable wearing all that skin and flesh...
Hades is ruler of the dead, wears the helm of darkness, has horses made of shadow, and fights wearing black armor with a crimson cape... and yet he is far from a villain. Sure, he's a bit of a grumpy jerk, but because this is based off Greek Mythology (i.e. The Unfavorite), that's a given. Ironically enough, he's actually the most honorable of the Big Three. And of course the movie MAKES HIM EVIL!!!
Nico as well. He even states that there's no place for him at camp, as Hades and all his children are shunned by most gods and demigods who believe the dark is, in fact, evil. Plays this trope perfectly straight, however, as he may be Tyson's only equal when it comes to Big Damn Heroes moments.
Codex Alera: The Marat, sort of, and definitely the Canim.
The Marat are cannibalistic Rubber Forehead Alien barbarians and at the start of the first book are thought of as implacable foes, but eventually many of them wind up friends to the main characters and allies to their nation, show surprising sophistication of philosophy and honor, and have no concept of lying.
The Canim are an even better fit. They are seven-foot-tall wolfmen whose magic is fueled by the blood of sentient beings. Warlike by nature, they enjoy warring against each other and have 11 different words for "enemy", one of which essentially translates to "Worthy Opponent" and substitutes for friendship with a member of another range or race (essentially "Some day we'll kill each other but not today, and no one else but me can do so"). Most of them are generally honorable and trustworthy, albeit in an alien fashion, all disdain the slavery practiced in the protagonists' homeland, and some become as close to friends with the human characters as possible. Even their Blood Magic-wielding ritualists eventually are shown to have some genuinely honorable, decent individuals amongst them who still practice the "Old Way" of shepherding the common folk and injuring or bleeding themselves to protect them.
The Howlers, who are, from a certain standpoint, the most innocent species that the kids meet. Unfortunately, "fun" means "killing the shit out of everything they see." They are a species of genetically engineered killing machines. It's just that they don't know that killing is wrong, and Crayak preserves their naivete by altering their collective memory.
Similarly, Hork-Bajir are seven-foot-tall anthropomorphic dinosaurs covered in blades. Said blades are used to scrape edible bark from trees, and they didn't even have a concept of war before the Yeerks turned their whole species into Puppet People foot-soldiers.
In the Incarnations of Immortality series, neither Death nor War nor even Evil is intrinsically evil—though their jobs are frequently unpleasant, and occasionally a particular Incarnation does turn out evil. Which one is evil at the time of the series? Good. Although maybe not really evil as much as Have You Seen My God?. Many characters think God is just honoring the Covenant (which supposedly said neither God nor the Devil will interfere in the affairs of mortals).
The Day Watch, so called because they struggle to keep the forces of Light from remaking the world in their image, honestly believe the world's current state is better than whatever utopia Light might make. Their primary focus is the protection of free will, and they can describe it in quite noble terms, contrasting it to Light's determinationto make everyone good. On the other hand, many members (particularly in the upper ranks) are selfish and hypocritical, concerned only with protecting their personal freedom at the expense of everyone else.
The struggle between Light and Dark in the novels is more of a clash of philosophies, Utilitarian versus Nietzschean rather than Good versus Evil, and both sides produce more than their fair share of bastards, though for different reasons. Let's put this way, Communism was one of the Light side's attempts at improving the world. Their "perfect" Communism was sabotaged by Geser, the head of the Moscow Night Watch, himself after getting a vision of the Bad Future: a dark, militarized world a hair trigger away from nuclear annihilation. This resulted in the deaths of hundreds of people, not to mention what happened after Stalin came to power.
So was Nazism. The world knows how that turned out.
In the Icarus Project series by Jackie Kessler and Caitlin Kittredge, mutants with Shadow-summoning powers are described as likely to succumb to darkness and insanity. However, the Shadow-wielding character Jet is a major superhero and media darling hailed as "New Chicago's savior, the Lady of Shadows" and is determined not to give in to the side effects that come with her powers. Her former childhood friend Iridium possesses Light-wielding powers and grew up to be a supervillain, or at least a ruthless vigilante.
In Digital Devil Story, the demon Kerberos is described as larger than a lion,with two rows of long, sharp fangs, the metallic feelers, striped like a tiger, and with heavy-looking tail plated with snakelike scales. It follows its master Nakajima around like a loyal, oversized puppy, even go so far as to fight the much stronger demon Loki on Nakajima's behalf. Twice.
The Moth-kinden in Adrian Tchaikovsky's Shadows of the Apt series call themselves "Children of the Dark" are grey of skin, hair and eyes (which are pupiless) and dress in grey but are neutral and isolationist rather than evil.
The work is mainly associated with Dark Is Evil, but also contains examples of this trope. Frodo says he trusts Aragorn on their first meeting despite his dark and shabby appearance because he believes an emissary of Sauron would try to make himself appear fair. The other Rangers of the North are often misliked by other Hobbits who aren't as thoughtful about it as Frodo for the same reason.
Also, Tom Bombadil mentions that he remembers when the dark under the stars was fearless, before the Dark Lord came from outside.
The Elves awoke in the darkness before the Sun and the Moon, and always love night more than the day, which belongs to humans. In LotR Dark Is Evil is the result of the corruption spread by Morgoth, rather than an innate quality of darkness itself. Well, except perhaps the Outer Darkness, which implicitly spawned Ungoliant on its own.
The official color of Gondor? Black. OK, "sable", but that's just heraldese for "tincture black".
ShadowClan of Warrior Cats may seem malevolent at first, and have their fair share of evil cats, but they are not all bad. The POV of the books favour ThunderClan, seen as ShadowClan's direct opposite (aka: archenemy), which does not help ShadowClan's reputation. Well, ShadowClan used to be evil. Now they're just The Rival.
Dyrnwyn the Black Sword from the Chronicles of Prydain is a subversion. While it is a powerful weapon of justice that can only be wielded by a truly good and noble person to strike down evil, it was originally a bright and shining blade. Its blade turned black when its first wielder murdered an innocent shepherd with it in a fit of rage. So while the sword itself is not evil, its dark appearance is a reminder that it once shed innocent blood.
The Land of the Night from Chronicles of the Emerged World is a land costantly covered by eternal magical darkness, but this spell was done in order to attempt to make the land hard to besiege. Also one of the main characters, Laio, is from that land and is one of the nicest folks.
Autumn Visits, another of Sergey Lukyanenko's novels, does something similar with the Champion of Darkness, although it is difficult to sympathize with a guy who kills women, children, and elderly. His goal appears to be to kill all Envoys (except himself), so that they do not influence humanity, letting them make their own choices. His methods, though, put him squarely into the villain category..
When the protagonist of Andrei Belyanin's My Wife Is A Witch duology travels to other dimensions, one of them is a world populated by dark creatures such as vampires, werewolves, warlocks, witches, most of whom are decent enough people with families and jobs. Granted, the first time he meets them, they try to kill him until he proves his power (apparently, his poetry has magical qualities in these dimensions) and fulfils the prophecy of a Witch's Husband (witches are normally too free-spirited to marry). This also becomes a problem in the second book, when his wife's cousin, who is obsessed with Sailor Moon, accidentally ends up in this world and starts attacking the so-called "evil" creatures, slaughtering entire families, as befitting her favorite character.
The inhabitants of Ixchel in A Wrinkle in Time look like hideous monsters but are actually kind and good. Aunt Beast may be the single nicest being in the whole book.
In Monster Hunter International the orcs look like well, orcs (warty grey green skin, yellow eyes, tusks, pointy ears), ride dire wolves and wear mostly black, but are definitely good guys.
Part of the theme of the Israeli children's book "חיית החושך" ("The Beast of Darkness") by Uri Orlev. The titular beast, who's full form is never really observed or described, is said to come from "the darkness between stars; the deepest darkness there is. It is extremely vulnerable to light (said to "shrink to a tiny size" during the day), but it grows to full size in the darkness can move to wherever shadows reach. It also has several other powers... The protagonist is initially afraid of it, but it turns out to be very friendly and supportive, using its powers and advice to help the protagonist deal with the death of his father (who died in one of Israel's many wars), his mother's re-marrying an old mutual friend of theirs whom the protagonist doesn't trust in the beginning, and the birth of his new sister (the Beast of Darkness tells the boy the baby's gender in secret long before the doctor's find out, having discovered it for itself by sneaking through the darkness in the mother's womb). Having helped the protagonist move on with his life, the Beast of Darkness leaves, maybe to find other children to help.
The Fallen Moon series fits this bill. The protagonist is a dark-haired undead northerner who worships the moon, can walk through shadows, and is prophesized to kill the champion of the Sun God in battle.
Of course, the southerners avert this, being fanatic rascists who believe if the northerners deserve to live at all, it is in slavery.
Very much in play in Brimstone Angels. Heroine Farideh is a tiefling- which means that she's part of a race conventional wisdom holds to be descended from devils and looks the part, complete with horns, a tail, and creepy Monochromatic Eyes. She's also a warlock, which means she gets her magic through a bargain with a supernatural being, in this case the cambiondevil Lorcan. Because of this, most people she meets assume she's Obviously Evil, even though she's actually a brave and moral character. Her twin sister Havilar gets somewhat less of it, both because Havilar is a Badass NormalAction Girl rather than a warlock, and because she's got a cheery, friendly demeanor while Farideh is broodier and angstier.
Nico from The Legend of Eli Monpress series is a demonseed whose abilities include the power to 'step through shadows' to effectively teleport. She always wears a dark coat, and is usually associated with dark colours. While the demon that infects her is obviously evil, Nico is one of the most selfless characters in the books. Interestingly, when the demon possesses her, her normally dark brown eyes glow yellow.
Dee is a dark elf priestess and one of the nicer girls in the dorm.
Mackenzie, who's supposed to be this horrible man-eating half-demon, is actually really nerdy and shy and wouldn't think of hurting someone... unless she forgets to drink virgin blood once a month, or comes in contact with a diabolic rage-inducing weapon, or someone tries to hurt Two, or... Well, the list goes on, but she regrets her actions after she regains control.
The Hobgoblin in the The Moomins book "The Hobgoblin's Hat/Finn Family Moomintroll" is dark, forbidding, sinister and obsessed with gathering rubies, not to mention that his lost hat produces all kinds of bizarre and bewildering transformations. He also enjoys pancakes and jam, attempts to buy rather than steal the gem he's coveted for a very long time, and grants a wish to everyone present as a way of cheering himself up.
The Wheel of Time has an organization called the Black Tower. It is an order of male channellers dressed in big black cloaks, who intensively study the uses of the One Power as a weapon and not much else, and must constantly fight against an evil corrupting curse not to become insane. Although the organization is, unsurprisingly, quite heavily infiltrated by darkfriends, the Black Tower as a whole and most of its members are actually on the side of the good guys, and are among the most efficient opponents to the Dark One and his minions.
Macon, being an Incubus, is of the Dark, but chose to side with the Light.
Also, as John Breed stated, there is Light in the Dark and Dark in the Light. So, it could be assumed that Genevieve, Ridley and Macon could do good things and help other because they were not completely evil.
In The Underland Chronicles, Gregor, the hero, wears black armour during the final battle, and his bond is black as well.
In Dark Heart, the heroine Myrren worships the evil god Vraxor and has powers based on dark magic, but is sickened by the thought of killing. Her father, Warde, is a feared military commander who's conquering the nations of the west on behalf of Vraxor's priesthood, but shows himself to be a devoted parent and a surprisingly kind and decent man.