The majority of anime/manga examples are themselves an example of the cultural differences between Japan and the US. Contrary to the Anglosphere, in the East, good guys wear black and bad guys wear white.
Black Jack, while morally ambiguous, is nonetheless a life-saving hero who dresses in a black suit and black opera cape and has mostly black hair. His archenemy Kiriko is an overenthusiastic euthanasia doctor and has eerie white hair.
In the Nightschool, there are demons, vampires, witches, and people with horns spikes and wings...and then you meet Genki Girl Rochelle, the cheerful Night keeper Sara, and Madam Chen, who just wants her coffee. In fact, most vampires are harmless pretty boys (until they become Rippers)
As in the video game, the Pokémon that look scary or "evil", like Houndoom, Shuppet, Duskull, and others, are just as capable of forming friendships with their trainers as any "cute" Pokémon, and frequently appear in perfectly normal settings. On more than one occasion, in fact, Ash and his friends were in fact helped out by a pack of Houndhours against Team Rocket.
A shining example is Ash's Gliscor; despite becoming more confident in its abilities since evolving, it retains signs of the hyper crybaby it was as a Gligar. However, it isn't a Dark type at all (its fierce design likely fooled everyone into thinking otherwise).
Or Muk, a Walking Wasteland that basically loves everybody. (It sure loves giving hugs.)
And then there's the tenth movie, Pokémon: The Rise of Darkrai. The title Pokémon, whose special abilities involve being able to create nightmares (and in the story, cause eternal nightmares that can only be cured with a Lunar Wing), turns out to be one of the good guys here. Actually ends up saving everyone. The lord of nightmares. Darkrai Is Not Evil! Well...usually.
This trope is probably felt even stronger in Japan, where the Dark type is instead named the Evil type.
Giratina had "666" symbolism on its body (6 spikes, 6 legs and 6 ribs). OK, he's not "dark" in the traditional sense, but he's a Ghost-type, and Ghost is usually associated with darkness...plus the Reverse World ain't exactly a place of eternal sunshine.
Giratina is actually a representation of antimatter in the same way that Palkia and Dialga are time and space respectively. He's most likely simply a ghost not because he is in any form 'dead' so much as alive in a sense somehow opposite to normal Pokémon.
Giratina could best be seen as the Pokémon version of an Eldritch Abomination. He's more highly aggressive than "evil" though.
The new Legendary Zekrom is completely black, contrasting with the all-white Reshiram. Presumably, that doesn't mean he's evil (His typing is Dragon/Electric).
Zekrom is actually, arguably, more heroic than Reshiram, because while Reshiram is representative of Truth, Zekrom stands for Ideals.
Bonus points if you bought the White version of the games, where the villains capture Reshiram and you capture Zekrom.
A lot of adaptations make the Psychic gym leader Sabrina to be a villain, or at least a mean and bad person. Pokémon Zensho and The Electric Tale of Pikachu keep her game personalities, or actually they keep her "Good" character alignment and amplify it; she's borderline Moe in both, and extremely kind in the latter.
Despite how nasty Takuto looks, and even though he did defeat Ash with a Darkrai and Latios, he's actually a pretty good guy, having given positive words to the protagonist.
Zorua and Zoroark, both Dark-types, look incredibly evil, with moves themed around "night". However, being based on kitsune, their actual personalities are more reclusive, protective and prone to pranks. Just...don't mess with their family.
In Digimon Tamers, this was the case post-Heel-Face Turn with Beelzebumon. Even though he was still a demon and had the element of darkness, the fact that he wasn't actually evil was part of what triggered his transformation into Blast Mode. This was backed up by a conversation between him as Impmon and Jianliang's sensei, who said he didn't sense an evil heart within him. The same applies to the Beelzebumon of Digimon Xros Wars, who was an outright noble heroic figure with an unfortunate history.
WereGarurumon can be counted simply by being a werewolf with a skull on his pants. He first debuted in the Nightmare Soldiers Pendulum virtual pet, which consisted of darkness and/or zombie-themed Digimon, but is of the Vaccine-types and is one of the main characters of Digimon Adventure.
Agunimon and his line also belong to the Nightmare Soldiers family.
Porunga, one of the wish-granting dragons from Dragon Ball Z, is a demonic, frightening-looking beast, but he's far nicer than even most regular dragons. When the heroes wished for everyone on Earth to be resurrected after Buu killed them, he went the extra mile and rebuilt all their cities and buildings free of charge. (He has been known to be a little sarcastic at times, however. When faced with someone who can't decide what to wish for, he once said, "wish for nothing three times so I can go". Most dragons would have threatened a mortal in that situation.)
We don't know for sure whether the aliens are all bad, though. Most of them are just trying to go about their everyday lives when they run afoul of the Gantz Team. Hell, the Oni aliens were fully functioning members of society.
While it is questionable as to how closely Alucard holds up to this trope, given that he'snotexactlyheroic, which some of his actions verge into Dark Is Evil territory, this is definitely played straight with Seras Victoria. Sure, she dresses in bright colors, but she's a vampire, and yet she values virtue and morality more than most other Hellsing operatives, even Integra Hellsing. Not that it stopped her from butchering Nazi vampires and then GRINDING ZORIN BLITZ'S FACE TO A WALL! But she is against killing people. Except the Major.
Nana from Elfen Lied is a diclonius, wears black, yet she is the most moral and pure out of all the characters, especially given the morality of the series.
The main character of 666 Satan is part demon, has a black and white motif with more emphasis, and constantly says that his goal is to rule the world. However, throughout the story he ends up doing more good than evil, accomplishing his goals more by gaining allies and saving people.
Out of the three supreme Oni siblings in Hell Teacher Nube, only middle brother Sekki is irredeemably evil. Baki and Minki start out this way, but are quickly brought to the side of good by Nube and remain heroic characters throughout. Similarly, a Western-style devil summoned by a witch (and fellow teacher at Nube's school) is actually a very nice guy, and Yukime's schoolmates at the Youkai High are great people, except for being, you know, horrible demons. (Ironically, at least one god is demonstrably evil.)
Evangeline of Mahou Sensei Negima! uses Dark magic, but she's more of a Noble Demon. Also two of the team members are partDemon, but are perfectly trustworthy (and probably some of the more honest of characters).
Not that choosing dark magic is without moral dilemmas. While dark is not inherently evil, it tends to intensify and magnify negative emotions (hate, anger) which can lead to evil. Negi very nearly succumbed in a recent chapter, and Rakan, the man who presented him with the choice between choosing dark or light magic, worries that Negi's inherent darkness (anger, thirst for revenge for his village, guilt), supplemented by the dark technique Negi learned, may lead him to be lost in darkness.
Also, turns out that because he's been using the technique, now he's turning into a demon. Of course, in Negima, Demons are Punch Clock Villains at worst, so it's not like he's actually becoming evil or anything.
Fran Madaraki of Franken Fran is a CuteFrankenstein's Monster. She has almost No Social Skills, and her day-to-day life can be best described as "macabre". But she's a brilliant surgeon (if unorthodox) whose entire existence is defined by helping people as best she can. Her servants also count - they look like the cast of a Universal Studios horror movie, but given they all recoil in terror from an actual horror movie...
Unfortunately, while Fran does mean well, the results of her experiments tend to end very badly for the people she is "helping" (although, in many cases, they did have it coming).
Her sister Veronica could also count. Sure, she loves to kill, but she does it as quickly as possible so they don't suffer. Of course, when she first see the outcome of a "Fran-periment", she does what any sane person would do: scream.
What about Skull Knight and Guts (known as the Black Swordsman) in Berserk? Sure, Guts isn't exactly by-the-book good, but he's willing to fight the real evil until the final consequences (to himself) must be worth something, not counting he's actually a Jerk with a Heart of Gold. The other is literally a Skeleton, as his name implies, and is frequently confused with Death itself, but is probably the most by-the-book Knight in Shining Armor in the whole universe of Berserk.
To be fair, in the world of Berserk, Guts is pretty much a Knight in Shining Armor when compared to everyone else in the world. In a less Crapsack World, he'd be an Anti-Hero at best, but considering where exactly he lives, he is Sir frickin' Gawain.
Angel Sanctuary has about all the main cast dressed in black robes and the like. And a lot of the good guys are demons or at least argueably non-holy creatures.
The title character of Yu-Gi-Oh! uses a Dark Magician deck. Also, the Pharaoh was known as "Yami" for most of the series, a name that literally means "darkness". There's also the Shadow Games; they often have a harsh penalty for the loser, but the one who initiates a Shadow Game must either make the rules completely fair or put himself at a disadvantage. Plus, they're generally only invoked against or by bad people anyway.
Two of Jonouchi's iconic monsters are Red-Eyes Black Dragon and Jinzo, both with DARK attributes. A minor monster of him is Panther Warrior, an EARTH monster.
To make it even more ironic, there are at least three cases where The Rival uses Light monsters. Yugi's rival Seto Kaiba uses Blue-Eyes White Dragon; in Yu-Gi-Oh! GX, Jun Manjoume uses Ojamas (and on occassion, the VWXYZ Union Machines), while Yuma's rival Kite uses the Photon monsters, which are ALL Light.
They go one further in Yu-Gi-Oh! GX, where Jaden Yuki's Superpowered Evil Side Haou the Supreme King is actually not that evil (nor, surprisingly, is the third season's antagonist, the demonic-looking Yubel); the former's power, known as the "gentle darkness" is meant to fight against the malicious Light of Destruction, while the latter chose to become a demon to protect Jaden's past self until he grew up enough to fight the Light off. Both were ultimately corrupted by the Light, though, hence why they were in full Face-Heel Turn mode upon their debut.
Jaden was never corrupted by the Light. Nor was Haou. Jaden chose to become evil in order to fight evil, which was a big misunderstanding, nothing more. There's no mention anywhere in all of GX of Jaden or Haou being corrupted by the Light.
That said, however, while both of Darkness' hosts were relatively nice people when they weren't trying to either set fire to Judai's friends or destroy the world via an Assimilation Plot, the entity itself was definitely not an example of this trope.
Darkness/Nightshroud twists thesetropes for all they're worth. Since dark in the Yu-Gi-Oh universe is stated to be a form of raw potential that is moulded by human hearts, Darkness/Nightshroud is implied to be created from The Sacred Darkness specifically because humanity thinks that Dark Is Evil.
In the manga version of GX, the headmistress of the Osiris Dorm is Midori Hibiki, a sweet, kind, and helpful teacher; her deck as a duelist, however, uses sinister-looking Darklords, Fallen Angels named after Biblical demons like Asmodeus and Superbia. (Ironically, the character who becomes her hated enemy is the villain who cursed her brother and put him in a coma, Reggie MacKenzie, a clear example of Light Is Not Good.)
In Yu-Gi-Oh! 5Ds, co-Lancers Jack and Crow run Archfiend and Blackwing decks respectively. The former has Red Dragon Archfiend (Red Demon's Dragon) as an ace monster, while the latter is centered around the Dark-typed Blackwing monsters. And teammate Aki's ace monster is Black Rose Dragon.
Interestingly, the six Signer dragons are three bright and three dark dragons, with two of them being LIGHT monsters and two of them being DARK monsters. And non of them are evil or less good.
Yuma in Yu-Gi-Oh! ZEXAL uses many Dark monsters too, like Gagaga Magician and Gagaga Girl.
In the manga version of Yu-Gi-Oh! ZEXAL, there was [[Grandpa Demetto. It's not know what he was, but he was a hideous-looking creature, a horrible-looking parody of Gepetto with an eye dangling from its socket and two long pins through his head. Despite this, he was a kindhearted creature who loved his friend Princess Cologne dearly, and when she was in danger of losing her soul due to failing to fulfill her end of the bargain she made with Dr. Faker, he gave her his soul to save her, sacrificing himself in the process.
Card Captor Sakura has both a "Shadow" card and a "The Dark" card, neither of which are evil.
The shinigami in Death Note look grotesque and kill humans to prolong their own lives. Despite this, they're a far cry from card-carrying villains. Most of them are morally neutral and easy to get along with. A few shinigami even fall in love with a human and risk their lives to protect her. On the other hand, they still kill humans (and gain the most if a human had a long life ahead of them) and Ryuk is arguably the evilest character in Death Note since he sets off all the terrible things that happen in Death NoteFor the Evulz.
The heroic Exorcists of D.Gray-Man are part of the Black Order. Despite the name and generally ominous, gloomy labyrinths that make up its headquarters, it's a good organization full of generally friendly people. Just don't ask aboutthe Second Exorcist Project.
However, the standard "dark = evil" is played straight in that the Akuma are made of "dark matter" and the Innocence is "white". Also, the evil Noah all have Dark Skin, well, most of the time anyway. And the only exorcist to go bad so far was Suman DARK.
But wasn't it the WHITE innocence that MADE him go "bad" and turn him into a...a...let's just leave it at that. Not to mention, all of the good Exorcists WEAR black.
In order to save Deedlit (and, indeed, all of Lodoss) in Record of Lodoss War, Parn had to wield both the Holy Sword as well as the Soulcrusher, symbolizing the necessary balance between Light and Dark.
Even more so: The 'Dark Knight' Ashram may appear to be utterly evil but indeed only seeks for a place for his people to live in peace (other than a cursed island, if possible). And his lover Pirotess isn't that much more evil than Deedlit, just less pure.
Despite the name, the Lord of Nightmares, from The Slayers, is not evil. She is, however, extremely powerful and dangerous, and the spells that draw on her power both count as Dangerous Forbidden Techniques.
Lampshaded in that a lot of characters do think that She is evil and the revelation that She is not is a pretty big reveal.
The Lord of Nightmares is more of a beyond morality kind of character. Her actions are thus not subject to being called good or evil. I suppose, however, if you want to look at it from the narrow-minded short term mortal view, that she chose not to unmake the world when she could have, to have been rather nice of her.
A truer example would probably be the Overworlders in Try - despite the dark scary armour and orignally worrying goal of summoning the Dark Lord of their own world (Darkstar), they actually serve the gods of their world and want to summon Darkstar to destroy him after he's merged with their god, gone berserk, and ravaged their own world.
That said, they range in "goodness," from Almayce and later Sirius who shows concern for the protagonists' world, to the more ruthless Erulogos, who's willing to let Darkstar wreak havoc on it if it means getting him out of their world.
The demons of YuYu Hakusho go all over the morality spectrum. While we have demons like Suzaku and Yomi that want to take over the human world and treat us as cattle, we also have outright good demons like Kurama, Yukina, and Raizen. In fact, his learning that not all demons were evil was half the reason for Sensui turning into a Nietzsche Wannabe. The other half was learning that Humans Are the Real Monsters.
It gets even better. At the end of the manga, it's revealed that most of the "trouble demons" were actually innocent Class D monsters that were brainwashed by the Spirit World so that they can make themselves look good by padding the amount of actual incidents that their detectives can solve, letting them get away with things like taking territories and putting up dimension barriers under the guise of doing it for the greater good. Actual demons with evil intent are extremely rare, with the majority of them doing the nasty stuff because humans forced them to do it. When that gets revealed, the barrier between the human world and demon world gets removed, and it's shown that both worlds are slowly but surely intermingling with each other in peace.
Even the ones who eat us are spectrumed. Yomi is exquisitely civilized (in a brutal demon lord way) but just does not care about us and things like 'rights'; Mukuro is gruff and does exactly as she pleases, which happens to include eating the meat she likes best; Yusuke's bald monk buddies can't apparently live on anything else and if they'd starved themselves while Raizen was busy doing so then they wouldn't have been able to take care of him...
In Naruto, the Tailed Beasts were very feared and hated by humans due to their freakish appearance and immense size and power. The villages have tried many times to obtain them as a display of military power and to prevent them from roaming free and presumably destroying human-occupied land. Legend says that they are born from malevolence and feed off of it, but recent chapters say otherwise. When the Sage of the Six Paths divided the Juubi's chakra into the tailed beasts, the newly-formed beasts inherited no hatred. They developed it when the humans, especially Madara Uchiha and Tobi, abused their power to suit their interests.
GaoGaiGar FINAL takes this trope home and cuddles it. GaoGaiGar was always black, so the OVA pits it against the clinical-white Palparepa, who has an A God Am I complex the size of the sun. Then, just to drive the point home, it depicts freeze-frames in the battle as between a white angel and a black demon. FINAL also created the final pair of Dragon Twins, KouRyu and AnRyu, who represent light and dark respectively, and combineinto TenRyuJin (that's Heaven Dragon God in kanji).
Genesic GaoGaiGar, the main mecha of the GaoGaiGar FINAL OVA and the true form of GaoGaiGar itself, is the literal God of Destruction, whose purpose to 'bring hope of a new start from zero'.
Hayate Yagami of Magical Girl Lyrical Nanoha. The Queen of the Night Sky and mistress of the Book of Darkness, she has six black wings, a mostly black motif, and her signature spell is a Sphere of Destruction made of pure darkness called Diabolic Emission. She is also the boss of the heroes and one of the nicest people you could ever meet.
Chrono Harlaown wears black armor (complete with Spikes of Villainy). He's one of the good guys (and Hayate's commanding officer). (In Lyrical Toy Box, precursor of the Nanoha series, he's the antagonist.)
Tohma Avenir from FORCE wears black and silver armor when Reacted and is infected with the Eclipse virus, which is responsible for empowering the current antagonists and making many people massive jerkasses. In spite of the infection, he is still a nice person who is trying to avoid letting the Eclipse take over.
The demons in SHUFFLE! are only demons in name. They're pretty much amiable people with long elven ears. Nerine and her father Forbessi exemplifies this well enough, these demons seems to be less rambunctious than the Gods' side (which consists a Genki Girl and a Bumbling Dad).
History's Strongest Disciple Kenichi has "Dou"-type martial arts, which are powered by rage and aggression (in contrast to "Sei"-type, which are more about skill and precision). It is stated that many practitioners of Dou martial arts are most likely to walk the path of destruction. However, Dou-type fighting in itself isn't regarded as evil, and Dou users who are gentle by nature (including two of Kenichi's masters and his love interest) don't usually fall to that path.
A more literal example would be in the opening of season 2, where Kenichi's uniform is dark gray, almost black, and Odin's apparel is pure white.
Umehito Nekozawa from Ouran High School Host Club is a fairly nice person who just happens to be allergic to any light that's not candlelight.
The Black Knights as a whole take this Up to Eleven, especially if the viewer has seen Gundam prior to watching the show. Let's see, they wear black uniforms with Face Concealing visors, pilot Cyber Cyclopses which are also colored black, have a leader who plays about half of the villain fashion tropes and not intrinsically evil though generally reserved for villain mannerism tropes in the book, have an Ace Pilot in a fast moving red mecha who is The Rival to a 17 year old kid who Fell into the Cockpit of a Super Prototype...
The Witches in Ojamajo Doremi almost always wear dark clothing and their world is (usually) only accessible at night. They're actually nice people (with some exceptions) who have their flaws.
Onpu Segawa is the resident Dark Magical Girl and has a purple motif. At first, she played around with Dark Is Evil and this trope since her reasons for using magic were selfish compared to the Ojamajos. Post-Heel-Face Turn, she is one of the nicest people you would ever meet.
Prince Shade/Eclipse from Fushigiboshi No Futago Hime wears dark clothing and comes off as a very shady person. He's actually the resident Anti-Hero. Moon Malia, his mother and the Queen of the Moon Kingdom, is a very benign ruler despite her choice of clothing. Finally, there's Boomo post-Heel-Face Turn; he retains his dark color and imp-like appearance despite his turning.
In Sailor Moon (which always plays Dark Is Evil straight with its Big Bad's), Hotaru may be Sailor Saturn, the Soldier of Destruction, but she isn't evil. In fact, she's very shy and sweet, and even though she's possessed when we first meet her, it's not her fault at all.
Tuxedo Mask could also fit to some extent. Particularly well noted in his former life as a prince, in which he wore dark clothes that are more usually attributed to villains; contrasts quite nicely with the princess's white dress.
Pluto is also a decent example. Not many realize that being the Guardian of the Underworld is part of her duties, as it plays second fiddle to her dealings with Time. The personal color on her Sailor Fuku is also black and her skin is shown to be darker then the others.
The manga version of Chrono Crusade toys with this. Chrono is always known as a Noble Demon, and he's actually a very sweet person with good intentions, despite being a demon, whose kin are actually a race of space aliens. The rest of the demons seem very evil at first, but Aion is actually a Well-Intentioned Extremist that has simply come to believe the only way to "fix" the world is to destroy it. He's actually a very nice guy...besides the whole evil plan thing. In fact, all the Sinners have far too complicated motivations to be called "evil". And even the rest of the demons are simply space aliens left without a home and lead astray because of truths hidden from them by leaders long dead. The anime version, however, plays most demons as far less complex.
Note that Aion's character design is 'light' themed and he generally wears white, and that YMMV on his character, since friend and brother and Well-Intentioned Extremist and what have you he is absolutely a Magnificent Bastard sadist on top of everything else, even in the manga. In the anime he's like the most powerful force in the universe or something. And he rips off Jesus' dying words and then comes back from the dead with a smirk after the Downer Ending.
DNAngel actually has a character named Dark—who, you guessed it, isn't evil, despite being a Phantom Thief with black wings.
The Aswad from Mai-Otome are considered enemies of the Otomes because they dress in dark colors and are able to control Slaves, just like the Schwarz. However, when Arika and Mashiro take refuge in one of their settlements out in the Black Valley, they learn by observing the Aswad's leader, Midori, that they aren't quite as evil or scary as she first believes.
The Shinigami from Bleach all dress in black, and while many of them are morally ambiguous (or, in at least one case, downright evil) the majority are decent people...particularly compared to the white-cladsoul eating death monsters on the other team. Most especially Ichigo, whose most powerful form is dressed in solid black, with a solid black sword, and fires off huge blasts of darkness as his most powerful attack...and he's the main hero.
Tite Kubo has stated that the white=death/black=life theme in Japan is in full-effect in Bleach. Fact: The manga was originally going to be titled "White" because of the prevalent theme of death (early, anyway), but Kubo scratched that and used "Bleach" instead because it held the same general idea and sounded a lot cooler.
Kubo really likes to lay on the solid black tones, too.
The Hell Chapter movie also does this with the realm of Hell itself. It seems like a horrible, cruel place, but one must remember that the people it tortures are evil sinners. Oh, and when four innocent people are wrongfully ensnared in its chains, it goes out of the way to ensure that they're set free and the one responsible is punished.
Ignoring the mere color scheme, not all the 'good guy' shinigami are all that good, nor are all the arrancar evil. Eventually a rather identifiable backstory is revealed for many Hollows where they ended up on the side they're on simply due to wanting to gain power to protect their companions, or merely to find companionship. Also Gin Ichimaru's smile, Zaraki Kenpachi's aggressiveness, scientist Mayuri's 'dissection' habits...
Old Man Zangetsu both plays the trope straight and later partly subverts it. He always wore a black cloak, and prior to the final arc, he was thought to be a personification of Ichigo's Zanpakuto, who for starters saved Ichigo during his battle with Kenpachi. Now it turns out that he's a personification of Ichigo's Quincy powers, taking the image of Yhwach as he appeared 1000 years prior, and had initially intended to kill Ichigo if he were to become a Shinigami. Thank goodness he changed his mind.
Kukuri in Mahoujin Guru Guru dresses in black robes, carries a staff with an eye on it, and is described as a "Dark Elemental." Her magic involves demon-summoning and is considered dark magic. However, while possessing many traits of the Black Magician Girl, Kukuri's personality is closer to that of the White Magician Girl. There is also a Dark Society of black magic practitioners who are allies of the heroes against the demon lord Giri.
In +Anima, Cooro can't help the fact that he has crow's wings, nor that everyone therefore assumes he's the angel of death. It just...happened.
Sacrifar, the ninth form of Rave Master's Ten Commandments sword is a Darkness-aligned blade that increases Haru's aggression. When Haru first tried to use it in a battle, its influence began taking over his body and mind. Later, however, it is revealed that this wasn't because the sword was evil, but was due to the fact that the Ten Commandments was forged specifically for Haru's predecessor, thus Haru could not wield it properly. Presumably Haru is able to use it safely after he gets a sword of his very own, but he never used it again after that incident.
Ogami of Code:Breaker has dark hair, dark clothes, a dark glove, and uses his powers to burn people to death on a regular basis. He's also very much a good guy, going to great lengths to protect his friends and allies.
Mixing this up a bit with Light Is Not Good, Ogami's sempai is very sinister and is usually seen reading bondage H-manga, but he can control light (in the form of a shibari rope, naturally) and is also on the side of good.
Karasu in Noein looks kind of creepy — long white hair, black robes, a perpetually snarly face, always angry, and he's played by Crispin Freeman...but he's just Yu all grown up, wanting to protect Haruka. His counterpart Noein is a Well-Intentioned Extremist however, who wants some kind of utopia or instrummentality.
Some of the chimeras of Fullmetal Alchemist, especially Zanpano and Jelso, whose "beast modes" are pretty ugly; the same probably applies to Alphonse Elric when his soul was attached to the armour as it is presently. Of course, this being a world where the bad guys are homunculi, Dark Is Evil is played fairly straight, and so is Light Is Not Good.
Van Hohenheim is quick to remind us the he's a monster; he still bends all his efforts toward saving people and acts jolly and clueless most of the time. His "son" Homunculus's original form, aped by his eldest "son" Pride, is the strongest Dark Is Evil in the series — but it is in turn just a piece of the darkness that exists beyond the Gate (which appears to be pretty much Hell).
Interestingly, Pride, a homunculus with shadow-based powers, has two weaknesses. One is obvious: light extreme enough to drown out shadows entirely renders him useless, briefly. The other, relevant to this trope (in a literal sense)? Darkness itself; with no light, he cannot cast shadows.
Greed takes anime!Lust's place in the manga as Homunculi-with-a-hidden-heart.
Soul Eater has Tsubaki's Uncanny Sword form, which had previously been used only by Weapons in her family who ended up turning into violent killers.
Lord Death and his son Death The Kid also fit this trope. Their nature could lead them to the same fate as many in their 'family', but both end up making a conscious effort to avoid this by siding with humanity.
Most obviously is Nagisa Misumi as Cure Black from Futari wa Pretty Cure, the only good Cure who wears a black costume. She summons the Black Thunder whenever she and Cure White uses any version of Marble Screw. Interestingly, both refer themselves as "Emissaries of Light".
The Mirage Pretty Cures from HeartCatch Pretty Cure! are the darker versions of the originals and they are the reflections of the originals' inner conflicts. However, they are not evil.
The Masked Cure Muse from Suite Pretty Cure ♪ wears a black costume to hide her identity from Mephisto and the other Cures, since her Cure form is just a Paper-Thin Disguise. And indeed, after Cure Muse unmasked herself and strips off her black costume - revealing her true, yellow costume by the way - Mephisto immediately recognizes her by her appearance which looks extremely similar to her younger self's appearance, since Cure Muse has Rapunzel Hair in her Cure form.
Averted with Seiren. She is a black cat and she was Hummy's best friend before her Face-Heel Turn, though it was actually brainwashing. However, after Seiren pulls a Heel-Face Turn and becoming Cure Beat (a blue Cure), she loses her ability to de-transform into her her cat form, being now stucked in her human form.
Black Jack, while morally ambiguous, is nonetheless a life-saving hero who dresses in a black suit and black opera cape and has mostly black hair. His archenemy Kiriko is an overenthusiastic euthanasia doctor and has eerie white hair.
Kageyama of Fairy Tail is proof that just because you are in a Dark Guild does not mean you are completely evil. Even though he uses magic that lets him manipulate his own shadow (most notably turning it into a bunch of snakes), he's misguided, but not totally evil.
Darkness magic is not automatically evil magic. Simon, one of the nicest characters, has Darkness magic as his primary magic. Mirajane and Jellal have Darkness power as their secondary ones.
Speaking of Mirajane, her Take Over magic allows her to transform into demons. She used to be a bad (but not evil!) girl, but after the incident with Lisanna, she becomes one of the nicest girls of the series.
José, the master of the (former) guild Phantom Lord, has Darkness magic as his primary one. He's not a nice guy, but he's at least not really evil. He's just cocky.
Rogue, the Shadow Dragon Slayer, is the probably the nicest member of Sabertooth. And he refuses to become an evil guy like his future self.
The God Slayers have black colored magic attacks. Neither Chelia nor Orga are evil, especially the former who has even Healing Hands. Zancrow on the other hand...
Gajeel, a guy with long black hair, was the most ruthless member of Phantom Lord, but he eventually finds the right path by joining Fairy Tail. With his magic he doesn't fit the trope, until eating Rogue's Shadow magic, becoming an Iron Shadow Dragon Slayer just like Natsu who became a Lightning Flame Dragon Slayer.
However, his most powerful Iron Dragon Slayer spells, the Metsuryu Ougi spells contain the Japanese word ''Gouma" which means Karma Demon.
Lets not forget Mystogan, at first he did seem rather untrustworthy, but overtime his drop-in drop-out appearances became more respected than feared to the point were even Laxus began to like him.
Frau from 07-Ghost is probably one of the most literal forms of this trope. As he and all the other ghosts for that matter are worshiped as the protectors of the church, even though they all take the form of their enemy, the feared death god Verloren. Frau even wields Verlorens Syth as a weapon and eats the souls of those he deems too wicked to return to heaven.
Father Abel Nightroad of Trinity Blood may have white hair, but he wears black habitually, and in his Cruznik form he has dark skin and black wings. His homicidal, genocidal, brother Cain wears white, has blond hair, and in Cruznik form has white wings and light skin.
Haiyore! Nyarko-san stars a number of characters who outright call themselves Malign Deities (in Japanese 邪神, jashin), bear the names of figures from the Cthulhu Mythos, and may in fact be the direct inspiration for said figuresnote It remains vague as to whether it was these characters, their relatives/ancestors, or completely unrelated members of their species who inspired Lovecraft. But looking at the specifics:
Finally we have Luhy Distone, a recurring character who's the closest fit the series has to Cthulhu himself. Though initially as an antagonist, she attributes this to her job with the Cthulhu Corporation, and after being fired opens up a takoyaki stand and befriends Mahiro, Nyarko, and their group. She even goes out of her way to bury the hatchet with Hasta, to whom she was rather harsh while playing the villainnote A Mythology Gag nod to the traditional enmity between Cthulhu and Hastur, and pulls off a Big Damn Heroes moment during the final battle of the 2012 series.
The magical girls in Puella Magi Madoka Magica are girls who made psuedo-Faustian bargains and essentially became liches whose Soul Jars eventually gestate into Eldritch Abominations. However, while there are most certainly evil ones out there, the majority of them are just territorial or opportunistic, with many being outright heroic, and the series consistently plays even the worst ones as being victims of circumstance. Colors also seem to be no guarantee of morality; Kazumi is one of the most unambiguously heroic girls, and wears a mainly black outfit, while Oriko, one of the most villainous, favors white.
The protagonists of The Big O. Roger has a black suit and black shades, his assistant Dorothy wears a black dress, and Norman the Butler also wears a black butler suit. The main antagonist, Gordon Rosewater, wears an all white suit.
When the series aired on Toonami, one commercial has the narrator state, "Good guys...still wear black."
This is a central theme of Umi Monogatari. Kanon's evil aura doesn't make her evil; it grants her immunity to Sedna's evil, the point of the shrine maiden's song is that darkness and light must coexist, and in the end, Sedna fits this, as she was created out of accumulated sadness in people's hearts.