The Yin principle of Chinese Mythology and Taoism. Meaning literally "darkness"/"shadow", not only is it vital for existence (and for medicine: a healthy mind and body need equal amounts of Yin and Yang), but it is arguably better than it's light counterpart, Yang, as it symbolises calmness and peace (as opposed to agressiveness and war).
Many of the protagonists of the various branches of the Mabinogion are the Welsh gods of Darkness.
Hades. Even though he is portrayed as a Satan analogue nowadays, in the original myths he was described as grim and stern, but not evil. Ancient Greeks were wary him more because of the natural fear of death and unknown, rather than him being particularly malicious. Hades was actually one of the few gods that didn't harm mankind directly, even proving willing to work with people, who ventured into his kingdom demanding something from him. He was also the giver of earthly wealth - both precious stones and metals and seeds. The worst thing he ever did was kidnap Persephone.
Hecate (goddess of witches and ghosts) helped Demeter search for Persephone and when Hera turned a slave-girl of Heracles' mother into a polecat for sabotaging her attempt to prevent Heracles' birth, Hecate adopted the polecat.
Pan swings between playing this trope straight and subverting it. He's a goat-like guy who is usually happy to play a pipe and dance in the woods at night, but then he also has a tendency to get moody and shriek at people who disturb him (this is where "panic" comes from - it's what people felt when they heard his cries). Still, he never hurt anyone.
Anubis and Osiris from the Egyptian Mythology, which are both death related deities that are good and righteous.
Often, it should be noted, due to age and windows not being cleaned. Clean stained glass dims light but does not dull it-one of the major reasons people began to use stained glass was to make churches more aesthetically pleasing. Which arguably makes it an even bigger subversion-darkening ordinary light precisely to make it and the space it fills holier and more beautiful.
And now the trope gets inverted again once you realize the above statement implies that "holier" and "more beautiful" is the same as being not evil.
Dark and gloomy is probably what all old buildings looked like at the time.
Dark is not always used as a metaphor for evil, as God is described as providing shade and night to comfort people in in the book of psalms as well as manifesting in darkness before he punishes evil by King David.
Also while angels look like Eldritch Abominations, they're good. (Not perfect, as Job alludes to them being capable of committing follies but still held to the standard of being holier than people)
In a more symbolic sense, consider that the most common symbol for Christianity, a cross, represents what was originally an instrument of torture, ultimate humiliation and execution. This gets even thicker if you're Catholic and grew up with crucifixes in your churches.
Hinduism has several entities that are associated with destruction but are not directly evil; Kali is such an example, even if she is mostly demonized nowadays, much like Hades. Its last reforms spawned more confusion.
Shiva as well: although he's a god of destruction, he's also a god of fertility (this is why his symbol is the distinctly phalliclingam is his symbol. As Shiv and the Grasshopper (The Second Jungle Book) says:
Shiv, who poured the harvest and made the winds to blow...
And Yama. Seriously he is the coolest guy ever, very neutral righteous. Also, he has made mankind, so show some respect! He was degraded from a king to a judge, isn't that bad enough for him already?
In the Lusitanian Mythology there was Ataegina, a goddess of the night that was also the goddess of Spring. Similar in some ways to Persephone, another benevolent goddess of the Spring and the Underworld, except that Ataegina wasn't married to anyone.
Santa Muerte. Almost unbelievable since she's considered a Catholic saint by a community in Mexico. True, Catholicism as a whole does not accept her canonically, but enough worship her that the movement is pretty much a de facto religious sect. Subverted in that a few of her followers use her to impose death on their enemies, though several other worshipers aren't that nasty.
In Celtic Mythology, the children of the god of death were believed to have come from the underworld to claim this one, driving out the Tuatha De Danaan in the process. They were also the first humans.
Many occult members who worship Satan believe that the devil and his demons do not necessarily represent evil.
Modern Satanism simply tries to free people from the power of symbols - to perceive that a dark room doesn't contain any more evil than a well-lit one and that a halo doesn't make a creature more good than horns. Classic demon-summoning occultists in turn were almost always under the opinion that they were using demons with God's power to do God's work, a belief-system based on the Biblical account under which God gave King Solomon the power over all demons to do good with.
Do notice, however, that Lucifer means "light bringer", although many experts in theology claim that he is a different entity from Satan. Also, some demons like Moloch were originally solar deities before Christianity took over.
In Lakota mythology, darkness is simply that which is irrational, contrasting to the light of reason. Inktomi is the embodiment of darkness in this sense, but he occasionally does heroic things, albeit always through trickery and deception.
Merlin, who technically was a half-demon and considered a good magic-user in a time when everything that people considered magic was associated with Satan.
In Islam, quite a lot of emphasis is put on the night. One ayah even describes the night as a soothing blanket. Israa al-Miraaj was a journey that took place during the night, from Mecca to Jerusalem to the seventh heaven. Qiyam al-Layl is a night prayer, and is the optional prayer with the most rewards. Similarly, Laylat al-Qadr ("Night of Power") is a night during the last third of Ramadan in which, if one prays during this night, it is better than if they had prayed for 1000 months. In the Islamic calendar, sundown marks the beginning of a new day, and not sunrise. During Ramadan, no food or water can be consumed by daylight; eating and drinking is only allowed at night. The association between the night and good things come naturally to desert people, as the daytime is a scorching-hot torture, but the night brings cool winds.
Hel from Norse Mythology. She just rules Helheim, which is where those who weren't cool enough for Valhalla but not sucky enough for Nifelheim go. She even offered to give Baldur back if everyone mourned for him.
Demons/daemons were not necessarily considered evil until around maybe as late as a thousand years ago. Before then, the general idea was that they were just fear-and-awe-inspiring beings of greater power than ordinary men could imagine, essentially somewhere between demi-gods and gods in power and often in the service of gods and other divine beings. Summoning a demon to perform a task was, at a basic level, no different than calling for a servant the king had given you authority over to ask them to do you a favor.
It should also be noted that, at one time, angels and demons were both daemons, the only distinction being that some were good and some were bad.
Played with by the black dogs of British folklore. On one hand a lot of them are supposedly malevolent but just as many are neutral or even benevolent. All three varieties are usually described as being extremely large, powerfully built dogs with red eyes and shaggy black fur (some accounts state that the fur is actually black in the 'absorbs all light' sense rather than normal glossy black dog fur) Additionally most of the supposed real-life sightings involve the black dog in question either ignoring the human present altogether or being somewhat friendly or at least non-aggressive. Even the more hostile encounters usually only involve someone getting a bad fright and/or being chased for a bit.