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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.
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.
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. 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.
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.
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.
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.