Louie and Ian Von Helson from Gaia Online, as they are vampires.
The Elves and Glombies too.
The Darkness Faeries in Neopets. Although even other fairies consider them evil, most of them are misunderstood and mischievious at worst, although they still seem to have an edge in the "evil" ratio as a group. There are many Neopians that even suspect that Queen Fyora herself is a Darkness Faerie promoted as queen, due to her name ending in the same sound as Jhudora and Jennumara, two Darkness Faeries (at least one of them, Jennumara, is actually evil. Jhudora might be just a bigass poser that might hug puppies when nobody else is looking... Or not).
One darkness faerie in Neoquest II states that they are not evil, just Chaotic Neutral.
Worm. Okay, it centres around villains whose only fully heroic member is the protagonist herself, but it is repeatedly shown that even at their worst none of The Undersiders are truly evil or anything close to it. However- unlike other such villains in the series- their powers are a collection of nightmare-inducing horrors that even includes someone with literal darkness powers. He is a villain in order to get money and a respectable facade so he can take care of his younger sister away from his extremely messed up mother. He worries about his lack of social awareness and is shown to forget how unpleasant his darkness is as he can see, hear and feel normally in it.
The Creepypasta "Love" features a haunting by a ghost that actually turns out to be benevolent.
To elaborate The protagonist's father was a Sergeant that died in the line of duty and the ghost was a loyal solider that died alongside him keeping a promise he made to him to protect his daughter should something ever happen to him. On her 18th birthday he deems his final order complete and leaves her a letter before crossing over.
One of the main characters, Orpheus, in the audio play Guiders of our Dreams is Guider, or controller of Darkness itself. He is surprisingly a very friendly guy, besides the fact that he could unleash all hell.
From Welcome to Night Vale, the titular town is associated with night, darkness, shadows, the moon, and the color purple. Sure, a lot of bad stuff happens there, but for the most part Night Vale's inhabitants are pretty friendly. It makes a nice contrast to the Light Is Not Good tendencies of the neighboring town, Desert Bluffs.
Night Vale's creator and destroyer, Huntokar is an interesting case, as she helped Night Vale survive to the point where it could become a town, but she later ended up accidentally destroying it in at least one reality. This is because she comes from the same ancient group of gods that includes the Glow Cloud, the Woman From Italy, the Distant Prince and the Good Boy; among these, she was the only one who didn't revel in creating destruction and chaos and madness.