Batman. The Dark Knight is often one of the best barometers of what the writer wants you to think is morally acceptable in all of comicdom, despite his black clothing, bat-motif, and fear-based methods.
DC Comics continuity has a realm called the Great Darkness, which is sometimes referred to as the Darklands or Shadowlands. To make a long story short, when God said "Let there be light," this inadvertently created something called the Great Evil Beast, a creature composed of darkness and shadow on par with God itself. While this creature did go on something of a small rampage on account of not knowing its own nature, when it got to the gates of the Silver City, it merged with God to create a sort of yin-yang creature. However, the part of reality where it had formed was left over, and is called the Great Darkness. Many heroes and villains in the DCU make use of this realm and its power to manipulate shadow and create shadow constructs.
The DC superheroine Nightshade has darkness-based powers, including the ability to create and manipulate darkness, and to create shadow-creatures.
Depending on the Writer. Oftentimes it's pretty clear that he's a psychopath who is only conveniently aimed at people that are (usually) worse than he is.
The Shade, one-time villain of the Golden Age Flash. He ended up as a mentor to Jack Knight, aka the hero Starman, so the Shade probably counts for this trope. He gained his power during a human-sacrifice-demon-summoning Gone Horribly Wrong (Or Right, depending on how you interpret the vague hints) in Victorian England that killed 104 people. Shade is probably far and away the most powerful of any of the DC characters that draw power from the Great Darkness, as not only is he ageless and immortal, but he has far more control over his shadow abilities and can directly travel between normal reality and the Great Darkness at will. Notably, he's been said to be capable of standing up to The Spectre (also known as the physical personification of the Wrath of God) and at one point, a future incarnation was able to transport Jack Knight centuries and light-years across time and space.
Nightcrawler is covered in indigo fur from head to toe, has pointed ears, fangs and a prehensile tail with a spade at the end, as well as the ability to teleport in a cloud of black smoke that smelled of brimstone, leading to more than a few demonic comparisons (even before that whole Azazel mess). He is also a devout Christian, a fan of Errol Flynn movies and one of the nicest guys in the Marvel Universe.
Trauma from Avengers: the Initiative is a half-demon who can shapeshift into a person's worst fear, invoking responses that range from a freakout session (Armory and Cloud 9) to reliving one's worst personal shame (Yellowjacket) to ending up in a mental institute (Trauma's mother). That being said, Trauma himself is a pretty nice guy who seems to have found a calling in helping people overcome their fears.
The Ghost Rider is a burning skeleton riding a motorcyle made of hellfire. He's also the hero of his story. And in one storyline is actually revealed to be an angel.
Hellboy. This quote is from the end of the movie, not the comic book, but it applies:
"What makes a man a man? A friend of mine once asked. It's the choices he makes. Not how he starts things, but how he finishes them."
Not that it's especially easy to find any actual light-aligned entities in his setting, and he tends to slaughter the dark ones he meets with extreme prejudice, although since he finds them by following the bodies there's a certain sampling bias and if it's not a whole army of skeletons or similar he treats folks like folks... mostly. But, as an Anti Anti Christ, he's trope-worthy for sure.
Blue Devil, especially after a Deal with the Devil turned him into an actual devil and he obtained a powerful Evil Weapon. He's still a superhero and a devoted churchgoer even though being in a church literally burns his flesh. Somewhat deconstructed when he learned that he had received a place in Hell's hierarchy as a Rhyming Devil because his heroic deeds have given Hell good publicity — he's made Hell "cool".
One of the only examples of this in the BIONICLE series is Takanuva after he survives a shadow leech attack. As for everything else, Greg Farshtey seems hell-bent on averting this trope.
In a literal sense, Onu-Matoran generally wear dark colored armor, live in nigh-unreachable caves and enjoy darkness, and some Earth Toa actually look pretty frightening (Onua with his humongous claws, likewise Nuparu, who also had a punk-themed mask decorated by spikes). Yet they're among the nicest of characters.
Subverted in Brian Bendis' Powers with Queen Noire. Although a good guy, the source of her powers certainly isn't. Which then proceeded to kill the entire team and them some.
The Creeper is a yellow skinned, green haired giggling madman who looks eerily similar to the Joker and possesses a laugh terrifying enough to physically paralyze anyone who hears it. He's also one of Gotham City's vigilantes and was present alongside the other heroes who came to oppose Hush following Batman's death, described by Dick Grayson as "trusted allies sworn to preserving my father's legacy". (Depending on the Writer, the Creeper is often perfectly rational, but pretending to be insane because it scares the willies out of criminals; Batman himself uses a different approach, but to much the same end result.)
The "Nega-Scott" in Scott Pilgrim does look like an evil doppelganger of the title character, but he's got a much more bigger and significant purpose than that. He's a manifestation of all the mistakes that Scott has made and is meant to make Scott learn from said mistakes to become a better person. As such, Nega-Scott is absorbed into Scott so that he could make a better influence on his girlfriend and his other friends.
Kaluu, an Evil Sorcerer and one-time foe of Doctor Strange, accompanies him on a mission to defeat the dark magic Strange had inadvertently loosed in the world. Over the course of their misadventure Strange was forced to admit that Kaluu was also a hero working on the side of good, even though his pragmatism and readiness to sacrifice some to save others bothered him.
Etrigan is basically the embodiment of this trope. He's a demon from hell, but he's still a good guy. Sometimes. It might be more accurate to say that he often falls into a kind of a "the enemy of my enemy is my friend" situation with the actual "good guys," and that they sometimes have compatible goals ... in the short term, at least.
Batman's Marvel counterpart, Daredevil, also counts. He dresses up like the Devil and inspires tremendous fear in criminals due to his intense bravery and vicious fighting style but is a hero who stands up for the oppressed both as a hero and civilian and sacrifices himself for others on multiple occasions.
The Rot in Swamp Thing was originally treated as a dark force of evil. It's really just the natural force of death and decay which is vital to the cycle of life corrupted by Anton Arcane.
In the comic version of Winx Club, a witch named Shilly is convinced by the Trix to make a love potion to break up Stella and Brandon (since the Trix were still going through their awkward "we want to be bad guys but aren't quite sure how" phase at this point). Once she realizes how miserable Stella is without Brandon (who has consequently fallen for her, due to the potion), she and Bloom make an antidote to the potion. She ended up being friendly with the Winx since then, though she didn't get that much face time after that story.
Nico from Runaways is fond of wearing black, homemade "goth" outfits, is the daughter of supervillians, has to cut herself to use her black magic powers, and would be pretty scary...if it weren't fact the fact she starts out as a Perky GothOrdinary High-School Student (albeit one who hardens as time goes on), wasn't the Team Mom, and wasn't very committed to doing good in order to counteract the mess her parents' superillianry caused in LA.
The Shadowdog from Hellblazer was the Guardian Entity that protected humanity from The Beast by attacking its human hosts (who were already dead due to the possession) before it could drive all mankind mad. Due to its fearsome appearance, its violent methods of dealing with the Beast's hosts, and the fact that it always showed up whenever the Beast started causing strife, people wrongly believed the Shadowdog was the threat.