The King Of Street Fighters has most of the characters from KOF who know Iori Yagami comment on this, saying that he's currently adopting this trope.
Blue Mary: "You don't quite understand what I mean. Seriously, when he started in the Ko F tournaments, he was focused on burning Kyo to a crisp. Never said a word to anyone and acted a lot like a puppy that got kicked around too much and grew up into a rabid dog just to pay the whole world back. Now, he's just...going along."
A main plot point on Dark Phoenix, a Harry Potter and Percy Jackson and the Olympians crossover. Most of Nico's powers are considered dark magic in the wizard community but he is generally (if not a little grumpy) Nice Guy. It's also later revealed that one of Nico's greatest fears is to be corrupted by his powers and become evil.
In The Tabula Avatar Universe it works out that many of the Dark deities of Faerun, when given the opportunity to grow beyond their status of two-dimensional game characters, network and make better choices.
Viconia, one of the Generally Evil Drow, has her alignment shift away from the extreme, thanks to good works and Character Growth. Even in canon, when left alone between games, she tries to live a simple, non-threatening life. As she's the most vital core of Shar's worship thanks to her nearness to the 'realness' matrix that is Dawn, this affects her patron goddess of shadows as well.
The Bridge has Princess Luna, par for the course is a caring diarch who won't standby when her citizenry is attacked. On the kaiju side we got the current Godzilla, the grown up "Junior" from the Heisei series. While extraordinarily powerful, a tad rough around the edges, and not abiding by Thou Shall Not Kill when the situation is dire enough; he never outgrew his Gentle Giant personality from his youth. After almost twenty years of protecting humanity from malign monsters later, and he's effectively become his world's Big Good by the time the crossover starts.
While dark is portrayed as a destructive and scary force in The Queen's Consort, it is not evil per say. Maleficent, as Queen of Night, is an expert on darkness and the magic that can harness it and she is looked upon the rest of fairy kind with both fear and respect.
Chiyo Ueda, the Super High School Level Medium, from Despair's Last Resort. She dresses in all black, has a talent involved with speaking to ghosts, and is rumored to have the ability to see when someone is close to death. Yet she's the most polite out of the students, and makes protective charms to keep the others safe.
Light: If he was kind enough to help me back to my room, the least I could do was be civil. So what if he looked like a pedophile? He was kind enough to help a complete stranger, the least I could do was give my thanks.
In The Dark Witch and the Necromancer Harry became known as the "Dark Avenger" for his liberal use of necromantic and other dark spells against Death Eaters. And when he wasn't slinging dark magic around, he acted like a Jerkass toward his friends and the Order.
If not a troll, Tara Gillesbie tried to make the protagonists from her fanfic, My Immortal, pretty much this, being goffs associated with darkness. Unfortunately for her, all she managed was to create extremely selfish and stupid self-inserts.
Thoroughly deconstructed in Harry Potter and the Methods of Rationality. Although most noteworthy evil wizards are referred to as Dark, including the Big Bad, much of the cast (especially Harry, Quirrell, anyone Slytherin) use it to refer instead to methodologies involving force, trickery, threat of force, blackmail, etc. Especially early on Harry finds that Dark tactics can be used to achieve good goals and to do things he couldn't accomplish without them; however, he eventually realizes that anything he achieves that way turns out to not be quite as good as it would if he'd done it without (for example, scaring a rumormonger straight ends Hermione's problem and may ultimately help the victim but angers Hermione and risks her reputation; going with an even darker plan of manipulation would have solved Hermione's problem but not helped the rumormonger at all. He realizes he should have just talked to her directly) and usually raises the stakes in ways that have unpleasant consequences. Too many Dark actions also affect people's perception of him. Even as he comes to understand this, though, he can't give up the sheer utility of his dark side entirely.
Discussed in this quote from Hermione.
But the thing that people forget sometimes, is that even though appearances can be misleading, they're usually not.
The Ash Ponies from The Ash are, essentially, what you'd get if ponies worshiped Nurgle without being evil: they act like creepy cultists, live in a Mordor that is so poisonous to ordinary ponies that having skin contact with the dust is the only thing that maybe won't kill you, their methods of recruitment includes exposing ponies to the soil of their abovementioned homeland or infecting them with the diseases which they themselves caught from the soil and survived which are both extremely painful, their appearance is a Brown Note that causes that causes a fight or flight response in most ponies and caused Rarity to nearly suffer a Freak Out! when trying to make a dress based on it and they managed to get Fluttershy to not want to be near them ever again in a week. But apart from that Diamond Dust seems to be the only one of them who is actually evil. They're just very creepy.
Luna as portrayed in Duel Nature is a borderline case. She does seem to care for the ponies around her even though she's bad at expressing it, but also seems confused by and disconnected from mortals and willing to do pretty terrible things when pressed.
Also, during the Final Battle with Fluttershy's Superpowered Evil Side, Princess Gaia/Nightmare Whisper, Fluttercruel forces herself out and is revealed to be a second Element of Kindness! The irony of this does not escape her.
Later on, we discover that the Elements of Chaos, despite belonging to Discord (or at least he can give them to ponies), actually have positive sides, as did the Rainbow of Darkness from which they originated. After Dark World!Twilight, Dark World!Applejack, and Dark World!Rarity are redeemed, they keep their Elements of Chaos while reawakening an Element of Harmony. It's explained that the Elements of Chaos were corrupted and 'incomplete' before, now they're purified and complete due to them having figured out their true meaning.
Dark Magic is not evil in and of itself, it's merely governed by emotions that are hard to control and therefore difficult for most to safely use without losing control of themselves. Those that can control those emotions, however, can use it safely. Sweetie Belle is one such pony.
The Draconequi, despite representing darker concepts like Anarchy and Destruction, are actually benevolent and the Rainbow of Darkness/Elements of Chaos is more collectively from them than Discord alone. They're Good Is Not Nice, sure, but they desire just as strongly as their Lawful counterpart the Alicorns for mortal life to thrive and grow, just in different ways. Even Strife, the most standoffish and cruel of the lot, only feels being challenged is necessary for life to grow, and hates the idea of killing for the sake of killing that serves no other purpose.
Havoc and Entropy, the Elders of the Draconequi, represent Fear and Hell, and The End and Nothingness respectfully. Despite this, both are Big Goods who have creation's best interests at heart in their own ways. Both them and their children come to help save the world from Discord's endgame personally, and Entropy even takes the bullet to protect the CMC from the Rewriting Reality wave that's unleashed, resulting in her avatar becoming Maud Pie, a mortal incarnation that is shown to soften her a good bit.
You Obey has a protagonist who isn't all that evil, despite being a changeling who interrogates ponies.
In Faith and Doubt, after a falling out with her friends, Twilight starts using black magic. Black magic can make a pony emotional and highstrung, but is doesn't automatically corrupt an individual. Twilight takes this idea to heart, that bad powers can be used for good, and soon Spike has been trained to harness his dragon-greed mode without slipping into the violent greed associated with it.
Princess Luna in RainbowDoubleDash's Lunaverse. The author actually notes that most of the ponies find the contrast of this trope with Corona's Light Is Not Good more than a bit disturbing. It's easy to think of the Princess of the Night as "spooky, mysterious, and a little bit evil". But now you have the Princess of Day, the very personification of the light and warmth of the life-giving Sun, turn against you, and you are only saved from her by the creepy Princess Of Night, whom you're still not quite sure you trust.
Clouded Sky has the protagonist Tobias Talltree, who is a "darkling", a Pokémon trainer who received a dark-type Pokémon (in his case, a Murkrow) as his starter. Despite him getting much contempt from various people he meets for this, he's still a perfectly kind, noble person. All of the other darklings shown throughout the story are generally shown as being nice, friendly people despite their affinity with the dark type.
The Houndoom in Goldenrod city are terrifying hellhounds. They broke Entei's pact to help May and her friends.
Dark-types in general tend to get portrayed as Combat Pragmatistwell-meaning jerks at worst. At best, they're loyal companions with cool attacks (just like everything else in Pokemon).
Cacturne from Total Pokemon Island is quiet and brooding, but he has a Hidden Heart of Gold. The only thing that troubles him is his dark side, which always threatens to get out and bring him to Dark Is Evil levels. Fortunately, he's finally tamed his dark side near the end of Total Pokemon World Tour.
Banette too. Despite his Dark and Troubled Past and his species' reputation, he's a relaxed guy and a good friend.
And Gengar. He's a creepy-looking Ghost-type, but he's really friendly and loves to party.
Sailor Moon: Legends of Lightstorm: The only two male heroes are dressed this way. Tuxedo Mask wears a black-and-red outfit, and Lightstorm wears an ultra-black set of body armor that makes him look a bit like an armored ninja. This doesn't stop them from being two of the biggest badasses on the side of good in the story.
Venus the Seedrian; a scarred cybrog Seedrian wearing a black leather combat outfit and armed with a Sinister Scythe. She has made it her mission to protect the remaining members of her race from Tsali at all costs. Subverted when she's possessed by Dark Tails.
Tsali and Maledict are deconstructions of this trope. Tsali is more brainwashed by his programming than truly evil and Maledict is basically a Well-Intentioned Extremist taken to its extreme.
The Marmolims who worship Maledict dress up in black robes and perform satanic rituals in his name. Despite that, they are all actually quite reasonable and friendly, and they immediately come to Sonic's aid.