The disturbing procedure of a dimension turning into nothing in Royal Heights is a every spec of life within the land being turned into clusters of golden butterflies and glowing dust while everyone screams in fear and agony.
"Now. A solid thing now, emitting the ghostly brightness of morning fog; for the Benefactor was not a being of darkness, not a creature of the shadows. No. Not darkness. Never of darkness. The Benefactor was a being of the brightest light, and it was here in the chamber with him, standing within arm's reach of him."
This has become a recent trend in Harry Potter fan fiction. Rather than the spells themselves being evil, the authors postulate that it is the intent behind them. This is largely an answer to questions about why they never kill the racist, terrorist, murdering wizards; once dark spells are no longer evil, you can start actually fighting without being as bad as they are.
Some examples: the kind of severing charm they use for cooking, Wingardium Leviosa hard into the ceiling until the neck breaks, or the old fairy tale favorite, Tarantallegra, until the heart gives out. These people are armed to kill from age eleven.
On a less literal level, the Houses Gryffindor, Hufflepuff, and Ravenclaw. While the Slytherins make up most of the bad guys in the actual novels, it is made quite clear that, just as not all present Slytherins are evil, the potential for assholes from the Houses that are seemingly more benevolent to exist is considerably large, and indeed a few show up, although not very prominent.
This is a common element in Gray fics; while the Dark end of the magical spectrum is not shown to be all hugs and misunderstood loners who want love, the Light side is often just as bad, or a little better/worse than the dark magicals. The gray characters tend to tell both to die and generally make it happen.
In Abandon by Batsutousai, Harry and Tom Riddle fall inlove and Harry and his friends joins the dark side. It is still clear that Tom is the evil one and the Death Eaters are still "the dark side", but as the story goes on Dumbledore and the light side appear more and more as manipulative bastards and the reader do not blame Harry for turning dark.
In Harry Potter and the Methods of Rationality, Harry finds that, when he becomes truly angry, he enters a coldly angry state, in which his mind works even better than it normally does (the purpose of the fic is Harry is incredibly smart, and incredibly well educated for his age in most non-magical fields.) When Snape's bullying pushes him into this cold state during Harry's first potions class, Harry asks how he would go about getting abusive teachers fired. Snape bullies him worse, and Harry tries to leave the classroom. When Snape locks the door, Harry escapes using a Time Turner, which he had been told not to use in any way that could indicate its purpose. When his anger leaves, he starts frantically thinking how to get himself out of trouble, and eventually pushes himself back into his coldly angry state in order to think clearly. He thus remembers that he was not completely in the wrong, remembers the other victims of Snape's bullying (who he had been told of previously,) and notes that his "light side" is the more selfish and cowardly state of mind.
In Heir there's Dumbledore-Leader of the Light, who has no problem with placing a child in an abusive household, using kids as pawns, or arranging for the deaths of his students.
There are quite a few Kingdom Hearts fics positing that, in order to complete the trifecta of Dark Heartless and Twilight Nobodies, the third faction of evil beings will be light-based and Knight Templar-ish.
The Kings of the Past and especially Ahadi are this in Scar's Samsara, since they are described as stars and use light as a weapon, but are at the very least non-good due to their methods and how conservative they are.
Chaos Is Very Good has an evil Celestia, Discord (who canonically casts bright lights when reality warping, and the fanfic mentions how "pristine" said light is) and the mesoamerican deity Tohil (who started the whole thing). Really, it's a good idea to go away from the light in that world...
Sunshine and Fire features a world where Celestia turned evil instead of Luna, defeated her, got rid of the moon and keeps the world trapped in an oppressive eternal day. Understandably, the citizens associate light with death, and darkness with safety.
RainbowDoubleDash's Lunaverse features a universe where Celestia became Corona, the Tyrant Sun, and was banished into the Sun by Princess Luna with the aid of the Elements of Harmony. And unlike in the canon plotline, the ponies did not forget their crazy evil princess. Even a thousand years after Corona's banishment, nopony will ever willingly be out-of-doors during the noon hour, gold is shunned, and ponies say go to the Sun the same way we say go to hell.
Played with in Sonic X: Dark Chaos. The Angel Federation stays neutral during a brutal civil war; Jesus decides to get involved, but sends his most powerful assassin Tephiroth to investigate. Neither of them are explicitly evil though, feeding into the setting's Gray and Gray Morality.
Played for Laughs in the fanfic series Sith Academy, starring Darth Maul as a Villain Protagonist. Between the frequent mind trick abuse, outrageous and inappropriate sexual hedonism, and practice of hauling non-conformers to a mental hospital and drugging/electro-shocking them into submission, the Jedi Order can only be described as blatantly, hilariously corrupt.
"Qui-Gon told me to quit seeing you," Obi-Wan sniffled. "Last time I defied him he sent me to the Jedi Happy Farm to be reprogrammed with Andy Griffith reruns." He shivered. Maul shivered as well. And people thought the Sith were cruel?