Waterbending in Avatar: The Last Airbender. It is powered by the Moon, and as a consequence it is stronger at night, it is associated with the Winter, and there's a Dangerous Forbidden Technique of bloodbending, but waterbenders are normal people like everyone else, and waterbender Katara is a main character; the swamp tribe in particular double counts because it is a subversion of Swamps Are Evil.
Asami Sato from the same series wears black and red, but she's one of the good guys and Mako's girlfriend.
Firebending too. Fire benders wear red and black and many of them are powered by the anger inside them, and it originated from dragons, but they are normal people too, outside of the Fire Nation royal family (excluding Iroh) and in fact the avatar before Aang was a Firebender.
Played with with the Dark spirits from the second season of Korra. On the one hand, they're on a rampage and being antagonistic, but as Unalaq explains, they are not inherently malevolent - no spirit is, according to him -, and are in fact reacting to people's disregard of nature, like Hei Bai in the previous series. Though the fact that they're being manipulated by Vaatu, THE dark spirit, muffles this quite a bit. Though he himself honours his deal with Unalaq with no fuss, so who knows.
We do see some non-angry spirits with dark aesthetics that are benevolent, however, like the one Bumi pacified with his flute and a dark, red eyed dragonfly-thing that accompanies Jinora in the Book 3 teaser.
Raven of Teen Titans, though she devotes a sizable amount of mental effort toward staying on the good side of the equation.
The title characters of Gargoyles may look like classical demons from Hell, but they are unambiguously heroes sworn to protect the innocent. (Well, most of them.)
This trope may only apply to the main characters, who were Scottish gargoyles. Gargoyles from other countries can have different appearances; the English ones resemble mythological beings like griffons.
Dib from Invader Zim raised network concerns because he looked like the kind of kid who would pull off a school shooting. He's the only person trying to save the Earth from an insane alien. (Although admittedly, he's not always nice about it, either.)
The Gaoul from Titan A.E. fit this trope nicely... creepy, red-and-black batlike aliens that really turn out to be a helpful mix of Giant Flyer and Red Shirt.
The Ruby Gloom cartoon intentionally exemplifies this trope. Perky Goth Ruby Gloom's friends include a two-headed Frankenstein's Monster, an animate skeleton, a banshee, a cyclops, a black cat, a bat, and three ravens. Despite being traditionally being monstrous or "dark", all are decidedly not evil, and very friendly, if a bit eccentric.
Other characters introduced along the way (including, among other things, a ghost, a mad scientist with the brains exposed and a carnivorous plant) are always examples of this trope if they are friendly. And there's an episode where the dark clouds covering the sky of their home place disappear; cue the oppressive hot sun.
Little Gloomy, which had similarities to Ruby Gloom. Sure, some of the characters were obnoxious, but there were only two particularly nasty ones in the lot. (The monster, for all his vows to destroy all life, did not seem to be one of them.)
The diesel engines in Thomas and Friends. Diesels are typically portrayed as evil; rude, heartless machines who want all steam engines scrapped. But several kind-hearted and friendly diesels have emerged, such as BoCo, Derek, and Rusty. Likewise, while steam engines are shown as the good characters, several aren't.
The Chaotic tv series features the Underworlders tribe of Creatures, who seriously play up the "Dark Beasts of the Netherworld" type for all it's worth, is host to some of the show's nastier monster badguys, like Lord Van Bloot, and it's leader, Chaor, is constantly organizing attacks against the Overworlder tribe. Yet, Chaor has been displayed honorable tendancies, and the Underworlder, H'earring, is practically Team Pet to Tom, Kaz, Peyton and Sarah. Furthermore, the Underworlders claim that the Overworlders were responsible for starting the war over the Cothica.
Just to point out that Chaotic is often all over the map with the tribes' and creature's morality. Yes the Underworlders are the most unashamedly morally grey tribe but the Overworlders have just as many problems. They've got a couple members who look and act like mindless thugs and some have a habit of arrogance and intolerance while not being afraid to Shoot the Dog while claiming to be moral guardian types. It's just that their Teamwork mechanic makes them seem nicer.
To really drive the point home, in one episode, Tom complains about how Midpedians (the bipedal, lizard-like tribe) are evil for attacking them in a previous episode. Peyton explains to him that no one tribe is all good or all evil, but that each has its' good & bad members. This comes to play when they're attacked by a scorpion-like Overworlder and saved by a Mipedian.
The Real Ghostbusters are typically hired by human clients to get rid of evil supernatural creatures, but some of the ghosts they've encountered are not evil, and are easily gotten rid of when the Ghostbusters help them complete their Unfinished Business. Other times, the supernatural creatures are the ones who hire the Ghostbusters, either to get rid of another supernatural being that really is evil, or to protect them from overzealous human villains.
In a Series Faux Nale of Fairly Oddparentsthe cosmic entity know as "the Darkness" turns out to have never been seeking trouble; everyone that saw it simply got scared and preemptively started filling it full of explosives. When Timmy decides to be the first one to send anything nice into it (namely a smile made from light coming from every planet in the solar system) it returns all the people it swallowed and its Killer Robots started hugging people.
The Pixar ShortPartly Cloudy follows a storm cloud who is only capable of making potentially dangerous creatures such as baby gators, porcupines or sharks for his Delivery Stork while all other clouds make cute little babies or puppies. Nevertheless, he is depicted as well-meaning, only wishing for companionship and not at all malevolent.
The minor character Mr. Green from the "Power Puff Girls" episode "Substitute Creature" looks like something from out of the gates of hell and looks like the kind of monster that destroy's things and harms people but he really is a sweet kindhearted nice guy who loves kids and is a good teacher.
Sid Philip's mutilated toys in Toy Story, despite being some of the creepiest things Pixar has ever rendered, are all pretty nice guys and have a knack for fixing things.
The toy version of Emperor Zurg (Buzz Lightyear's archnemesis) in Toy Story 2 would probably count. The real reason why he appears evil is because he thinks he's evil, believing that he is the real Zurg, just like how Buzz himself thinks that he is the real Buzz. The toy Zurg is actually very friendly.
If not Affably Evil, the Griffin from Quest for Camelot could arguably count. He's pretty much just the bad guy's pet, who ends up as being quite sympathetic for his Butt Monkey status, as the movie pretty much only shows him suffer in a way or another. The worst thing he did was his attempt to get revenge on the good guy's falcon (and getting burned by a siamese twins dragon for that), but then again he was asking for it.
Disney's Tarzan movie uses this along with Light Is Not Good with symbolization with the lighting. Deep shadows represent being hidden and well protected, while sunny areas resemble being vulnerable and out in the open.
Oddly enough, the zombies in Scooby-Doo on Zombie Island. Indeed, it turns out the cat demon creatures (aka, the true forms of their 'hosts' whose mansion they were staying at) are the villains, and trying to kill them for some form of life energy (and the zombies were the remains of the people the villains had killed in the hundreds of years before the gang arrived, and were trying to warn them about the villains). After the demons are killed, the zombies simply fall apart with their souls at rest, and the ghost of one of the Confederate soldiers who they'd seen in their earlier camera footage on the island thanks them.
However, some of the zombies weren't nice people when they were alive, as for instance the pirates responsible for killing the original settlers of the island.
Speaking of Scooby-Doo, how about Scooby-Doo and the Ghoul School? The girls of the eponymous school are all quite nice and friendly, and even their father (including the likes of The Mummy, Dracula, and The Wolf Man) are nice, if frighteningly protective of their daughters. The only really evil monsters to appear in the entire thing are Revolta and her minions.
See the Real Life page for more, but in Scooby-Doo! and the Witch's Ghost, Wicca is portrayed as good and its even gone into detail as to the fact they're very different from witches. Of course the 'Wiccan' they thought they were clearing the name of was actually an evil witch, but Wiccans were the ones who imprisoned her inside her own spell book and only a Wiccan could imprison her again. The Hex Girls (introduced in this movie) also play this trope; they dress like vampires for their act, but are actually three really nice girls and love the environment. They even help the Gang everytime they meet, and their leader is the one to banish Sarah the witch back into her prison.
This is actually lampshaded in their song "Earth, Win, Fire, & Air", with the lyric "we may look bad, but we don't care."
The Web Riders in ReBoot. Sure they fight the heroes and look creepy, but they're actually quite nice and helpful once you get to know them. They weren't fighting the heroes because they were evil or malicious, but because they were defending their herd of Web Creatures from the Net invaders.
Disney plays with its portrayal of villains in The Lion King 2: Simba's Pride. Kovu and the other Outlands lions are drawn exactly like Scar (lean build, dark coloring, pointed facial features), but only Zira is actually evil. Especially true for Kovu, who looks like a more muscular version of Scar, and even gets a similar scar after a while
In He-Man and the Masters of the Universe (1983), Castle Grayskull is just about the creepiest looking piece of architecture any villain could ever hope to design. Yet the place is always presented unambiguously as a source of power for good. Presumably, its appearance isn't really supposed to look evil... Just Bad Ass.
The 2002 version has a backstory that reveals that the castle was truly named after it's original owner, King Greyskull, a great hero and the true source of He-Man's power. (In fact, when Adam chants "By the power of Greyskull", he's actually calling on King Greyskull's power.)
In the 2002 animated series episode "King Randor", Adam and Man-At-Arms travel to the underground land of Subternia to negotiate between two races, one of which is a fearsome-looking tribe of bat people that a freaked Adam nearly pulls his sword on before Duncan stops him. Despite their appearance they're very friendly towards the visitors and Randor is greeted warmly by their king Lord Dactus. There's a funny moment of Not So Different when Adam expresses disbelief that Dactus is really their king and Dactus gently calls him on it.
Randor: I apologize for my son...
Dactus: I've been apologizing for mine for years! (they laugh as Adam and Man-At-Arms give each other wry looks)
Princess Luna is the ruler of the night, but isn't evil. Her Big Entrance in "Luna Eclipsed" pretty much has about every villain appearance trope you could imagine... when she comes to meet the citizens and show that she's no longer evil as in the Nightmare Moon persona that had previously taken over her for a thousand years. None of it is really helping her case, including her time of arrival during the night at Nightmare Night, a local version of Halloween centered around Nightmare Moon.
This has been confirmed as of "Princess Twilight Sparkle Part 2" to be alicorn magic. All alicorns the show has portrayed so far have been good.
Another example would be the zebra Zecora. She lives in a hut deep in a dark forest full of spooky monsters, speaks in rhyme, and collects herbs for brewing natural remedies (or in the townsponies' eyes, evil witchcraft before she's proven to be good). Despite this, she has never shown any ill intent towards anyone or acted threatening. In fact, the moral of the episode where she makes her first appearance, "Bridle Gossip", is "Don't judge a book by its cover."
While the first of the My Little Pony TV Specials has Dark Is Evil in the form of Tirak, it also has Scorpan, an Anti-Villain who is just a protective friend/parental figure who serves Tirak only for the safety of Spike and is otherwise a nice guy, despite looking like a demonic ape-man. Same goes for the next one, where the reptilian Rep is a reluctant minion who only serves Catrina because he cared for her before she went bad.
Like his comic counterpart, the demon-like Nightcrawler fits this trope to a T in X-Men: Evolution. In fact, he's probably the most lighthearted character on the show.
The film adaptation of Watership Down does this with the Black Rabbit. In the book he is a dark omen of death, pretty much the grim reaper for rabbits. In the film he is merged with El-ahrairah, a rabbit folklore hero. At the end of the film he appears before an old Hazel and invites him to join his Owsla. The two depart peacefully into the afterlife.
Lydia Deetz of Beetlejuice. In the movie, she was a moody, depressed and suicidal goth. The cartoon still has her as a goth, but here she's sweet, perky and creative. Her best friend is a ghost everyone else despises.
This becomes a minor sub-theme of Winx Club after the first season; once the Trix are gone, the witches of Cloud Tower start acting nicer to fairies. It turns out that, despite being powered by darkness and negative emotions, most witches aren't really bad people; the Trix just had a way of bringing out the worst in people, especially since they were the strongest kids at Cloud Tower.
Total Drama Island (and the following seasons) has Gwen. She's a snarky, cynical girl who dresses entirely in black and green, and is not afraid to point out when the other contestants are acting stupid. But as the episodes go on, it becomes apparent that she's one of the nicest characters on the show- she just takes a while to warm up, that's all.
Casper The Friendly Ghost also counts. Unlike other ghosts who scare people, he wants to be friends will everyone.
In the "American Dad!" episode "Minstrel Krampus" despite him looking like an evil demon and his tendency to kidnap children, Krampus is actually a very nice guy he kidnaps the children to show them the errors of their ways and teaches them not to be spoiled, on the other hand his mortal enemy Santa Claus whom the Smith's tangled with before is the true villain as he encourages the kid's bratty behavior and gives more toys to the spoiled kids regardless if they were good.