First, there is House Stark itself - a family of unshaven, dark-haired frontiersmen from the bleak, murderous North who dress in black pelts and have a snarling wolf on black cloth for a sigil... yet they're, unambiguously, the primary protagonists and heroes of the story, being one of the last families in Westeros that still puts Honour Before Reason.
Like in the original, the Night's Watch fits the bill perfectly. Conscripted outlaws, thugs and dishonoured nobles who don black armour don't paint a very friendly image, yet they are a Lawful Neutral force that forms the first line of defence against the Chaotic Neutral and Chaotic Evil powers that lurk beyond the Wall.
Melisandre likes to portray the religion of Light as Light is Good, but is actually at best a fickle and extremely ambiguous magic force.
Brynden "Blackfish" also dresses mainly in black armour and is a bit of a bully, but he is far from evil.
The Addams Family comprise of a variety of Horror Tropes, and appear highly sinister, but they hardly ever do anything that could be considered evil. They are, in fact, for the most part perfectly friendly and decent people (probably the healthiest family on TV when it first aired, and perhaps the most Happily Married too), if more than a bit weird and possessing unquestionably morbid and bizarre tastes.
The Munsters are a family of popular Hollywood monsters that act like your average Dom Com type family.
Irish children's programme The Morbegs had a whole episode centred around the "festival of darkness" that the Morbegs brought to Ireland from Morbegland. The human host of the day was afraid of the dark, but as the Morbegs said, "Don't fear the darkness! It's not bad, it's just different!"
The British show Being Human plays with this, as the main characters are a vampire, a werewolf and a ghost, all of whom just want to do their jobs, go down to the pub and be friends.
Although it's shown that most of the other vampires are very dangerous. While other werewolves just seem to try to get along on their own, Tully at least is shown to somewhat unbalanced (although this is probably owing more to being lonely than being a werewolf). Pretty much all the ghosts shown are perfectly nice people.
It's safe to say that 99% of the demons are evil but they make a good point of showing that some of even the more evil-looking demons are actually good guys. Clem (the loose-skinned but amiable slacker demon from Buffy) is an obvious example. As well as Lorne, an interdimensional green demon with red eyes and horns who was from a Proud Warrior Race... and the White Sheep of his clan. Skip, though originally fitting the trope, later counts as a subversion.
Angel himself is a vampire, but he's (usually) a good guy, if very, very broody, and he's the hero of his series.
"In My Time of Dying": Dean is on the verge of death and has become something like a ghost wandering the hospital. He sees a ghostly specter that seems to be trying to kill him and another patient. He meets a girl who seems to be in his same situation, but it turns out to be the Reaper he saw. She took a human form to be able to talk to him, and she turns out to be very sympathetic to his situation, but gently explains that he might become an angry spirit if he doesn't follow her into the afterlife.
"Bloodlust": Sam and Dean encounter another hunter, Gordon Walker, who is working a case trying to take out a nest of vampires. The twist is that it turns out that the vampires are the good guys in this scenario and have no interest in killing anybody, while Gordon is an Ax-CrazySoft-Spoken Sadist who just wants all monsters to die and doesn't care at all if innocent blood has to be shed in the process.
Sam himself is an example of this trope as one of the demon Azazel's Special Children, a group of people who developed psychic powers from being fed Azazel's blood at six months old. He does start to verge on Knight Templar in S4 when he embraces his psychic powers and starts fuelling them by working with demons and drinking their blood, but even then, he was still doing it with good intentions, as it gave him the ability to exorcise and eventually kill demons without killing the people they're possessing. Also, Andrew Gallagher, another one of the Special Children who, while mischievous, is a genuinely good person.
"Man's Best Friend With Benefits" introduces James Frampton, a witch who, in his familiar's words, "has used his powers for nothing but good", and who saved the Winchesters' lives in a Noodle Incident involving a lunatic alchemist.
The Antichrist, Jesse Turner, is a genuinely sweet kid who has no idea the kind of damage his mere existence causes. When he learns of the power he has, he runs away to Australia to avoid the Apocalypse.
While ghosts are generally evil, there are exceptions, like Mary Winchester in "Home", the Death Omen Claire Becker in "The Usual Suspects", Molly McNamara from "Roadkill", the ghosts in "Hollywood Babylon" (who were murderers, but only because they were bound against their will by a human occultist), Bobby Singer, and Kevin Tran.
Season 8 introduces a vampire named Benny whom Dean befriends while in Purgatory. While when he first appears in Purgatory he makes clear that he's a monster who's only helping Dean for personal gain, he shows while on Earth that since he last died, he really has grown a conscience and ultimately sacrifices his own life to save Sam and Bobby.
Garth is every bit as friendly as a werewolf as he was when he was human.
It's a subject of hot debate both in- and out-of-universe whether Amy Pond, the kitsune from "The Girl Next Door", falls under this. While she did kill a few people, she had a good reason for it (her son had a life-threatening ailment that could only be cured by eating freshly-killed human brains), and they all arguably deserved it.
The pishtaco Maritza in "The Purge", who uses her fat-sucking ability to help the already obese get rid of excess weight.
Dr. Eleanor Visyak, one of the few benevolent creatures to come out of Purgatory.
Averted and subverted throughout Teen Wolf, as there are werewolves who are more good/neutral, werewolves who are bad, creatures that are involuntarily evil, people that are purely evil, and so on.
Rescue Ink is a show about Bad Ass Biker type guys with hot rods and tattoos, some even with past jail time... who rescue helpless and abused animals.
In one episode of Criminal Minds a body shows up in a forest near a small town. The pentacle and candle wax nearby suggest Satanism, and the finger of suspicion falls on the local teenage Satanist group the Lords Of Destruction and their college-age leader. As it turns out, not only are the LOD innocent, they're the most normal and well-adjusted kids in town, since they're the only ones who didn't spend the last year watching a stranger's body decay for fun.
one episode features a young boy who is being followed around by ravens who turn into creepy-looking black-clad people. Turns out the ravens are the good guys, and they're following him to protect him from the real bad guy, the boy's teacher.
From The Dresden Files novels, Rashid the Gatekeeper. Dresses in dark tones, we don't actually see his face, but is one of the friendlier members of the Senior Council and has given Harry advice and support. As of "Cold Days", the truth is evident. His title of "The Gatekeeper" is explained to be a horrifying burden. Rashid and those working with him are the only thing standing between the mortal plane and every nightmare Lovecraft ever had.
Kamen Rider Raia from Kamen Rider Ryuki has a Contract Monster named "Evildiver", and thus by extension most of his equipment is prefaced by the word (Evilvisor, Evil Whip). However, he's actually a very honorable and noble person who is one of Ryuki's few allies in the Rider War.
In Ryuki's American Adaption Kamen Rider Dragon Knight Kamen Rider Onyx a black version of Dragon Knight was assumed evil since its Japanese Version Ryuga was evil, and the Evil Twin trope in general, and that Kit had nightmares of the armor trying to destroy him, or himself as Onyx venting Len and Kase, making him understandably reluctant to use it when Eubulon handed the deck to him. However when Kit took the Onyx deck and armor it didn't corrupt him as he feared it would and it showed as Kit used it to fight Xaviax's forces until Adam his mirror twin gave him the Dragon Knight deck in the finale (after the final battle. He actually spends the entire final arc as Onyx, and never wears the Dragon Knight armor again after Xaviax takes it in back in "Xaviax's Wrath.")
Interestingly, it's a straight reversal of the usual situation: Adam is the Evil Twin who'd betrayed the Riders before, and is now The Mole, pretending to have been a victim of Xaviax's manipulations and not truly a traitor. Kit is The Hero and holder of the Dragon Knight powers for most of the series, though Adam was the first Dragon Knight offscreen. This makes KRDK quite likely the only time you've ever seen the original red-clad hero meet a black repaint of himself from another dimension... and you're rooting for the latter, not the former.
While Ryuki and Dragon Knight have very different plots, Raia's counterpart Sting is also a true hero in a series where most Riders are out for themselves. The Japanese name for his Advent Beast, Evildiver, is kept (most monster names aren't mentioned onscreen, but we get a very good look at the Evildiver advent card more than once.)
Also, Len, Kamen Rider Wing Knight. He is scary guy in black/dark blue armor with bat Advent Beast. Until you get to know him. Actually, Len is nice guy, who will go to hell and back to save someone dear to him. He just doesn´t show it to most people.
The Dark Kiva armor in Kamen Rider Kiva is used by three people: King (the Big Bad), Otoya (who's good through and through), and Taiga (who is antagonistic but not evil and eventually becomes a good guy). Kivat the 2nd, who provides the Dark Kiva powers, isn't a bad person himself; he only goes along with King because he's loyal to the guy's wife, and pulls a Heel–Face Turn when she does, further prompted by seeing his Kid from the Future Kivat the 3rd partnered with Otoya's Kid from the Future Wataru.
Kiva stands for King Vampire but he's the good guy. Also, all his buddies are based off horror movie monsters but help him with protecting humans. Mind you, they weren't so good in the past, but over flashbacks we get to see how they became good guys.
Kotaro Minami AKA Kamen Rider Black. He's chosen to be one of the leaders of the Gorgom cult to eventually rule the world and his transformed form is majorly black colored. Instead, he uses his power to destroy Gorgom and protect humans. His rival Shadow Moon provides a nice contrast with silverish white color scheme.
Kamen Rider Kuuga has his Ultimate Form which, in its 'normal' state (fueled by anger) could cause the End of the World as We Know It and could destroy the planet with one Rider Kick. Also, it and his previous form (Amazing Mighty), are black in color. However, Kuuga uses them to fight the Gurongi and save the world.
It also gives the finger to Red Eyes, Take Warning, as when it's not fueled by anger, Ultimate Kuuga's eyepieces go from black to the standard red.
In Kamen Rider Decade, Rising Ultimate Kuuga is gold, but looks freaking scary and is covered with Spikes of Villainy. It was a bad thing only at first when the bad guys had forced him into that form and are controlling him. When he is himself again, we again get to see him go from evil and black-eyed to benign and red-eyed, and he goes on to help the other Riders do battle with Shadow Moon and later the Neo Organism.
The Ninth, played by Christopher Eccleston, wears a black leather jacket and had a very short military-style haircut — prior to this most Doctors wore very colorful outfits and funny hairdos. Despite his dark appearance, he's still as quirky as any other incarnation of the Doctor. He's not exactly evil, but he's definitely much darker than the other incarnationsin personality as well as appearance. This darker side is most apparent in "Dalek", and when this darker side manifests itself, it's almost scary:
Dalek:I am alone in the universe. The Doctor: Yep. (bitter smile) Dalek:So are you. (the Doctor's smile slips) We are the same. The Doctor: We're not the same! I'm not... no, wait. Maybe we are. You're right, yeah, okay. You've got a point. Because I know what to do. I know what should happen. I know what you deserve. (sadistic grin) Exterminate! (yanks down the shock lever) Dalek: (screaming) Have pity! The Doctor: Why should I? You never did! (turns it up further)
The Twelfth Doctor, played by Peter Capaldi, is a stark contrast to the goofy, light-hearted Eleventh (Matt Smith). Twelve has a stoic, intimidating face with a constantly-furrowed, bushy brow and a perpetually unhappy expression. Gone are the bow-ties and fez hats: Twelve prefers a dark blue Badass Longcoat. His goofy sense of humour has been replaced by a very dry wit. And like Nine, his personality has darkened into The Stoic. Twelve's first Dalek story, "Into the Dalek", hearkens back to Nine's encounter, with the Not So Different question raised once more. Despite this drastic change, and his own doubts about his nature, Twelve is still fundamentally a good person and notably remains Friend to All Children (though he's more prickly about it), and he still cares deeply for the people he considers his friends. It's just a shame that who counts as "his friends" is limited only to Clara as of the end of Series 8.
12 is very much a Knight in Sour Armor. If you were to meet him, (a) he'd do everything he could to save your butt, and (b) you'd still want to punch him much of the time. "Mummy on the Orient Express" is a prime example of this, as he didn't display the least bit of sympathy when someone was targeted by the mummy (it can only be seen by its target and kills precisely at the 66 second mark) and kept telling him to describe it so that others could be saved, and later lies to manipulate the person he expects its next target to be to get them where he needed them to be. But it turns out that he needed to do that so he could redirect it to target him, risking his life on being able to figure out how to stop the creature in 66 seconds or less. And he does. As of his second season he's stopped insulting people just for the hell of it, but he still ain't warm and cuddly.
The Sarah Jane Adventures: In "The Mad Woman in the Attic", Eve is a redskinned alien girl with a disturbing hairdo who mind-controls her "friends" into endlessly riding the rides of an abandoned fairground. And then we find out she's an orphan and refugee from the Time War who doesn't know any better, and that she's actually sweet and kind.
Played fatally for laughs in this SNLskit. Heaven's commitment to helping prayers is indeed doubtful when the messenger is Christopher Walken adorned in black.
Played straight in a episode of CSI, when a teacher is telling Grissom about a student who creeps her out badly. She points toward the lockers, and Grissom assumes she means the Goth boy there. The Goth boy walks away with an airy "Hey teach," as he passes them, revealing the preppy boy behind him who's the one the teacher was really referring to. It turns out there's very good reason the teacher was creeped out by Preppy Boy.
In Charmed, the three (at a time) main characters are dark-haired witches, but they're the heroes in the series, fighting against the forces of evil.
Of course, they go by the Wiccan definition of the word 'witch,' and Wiccan philosophy centres around doing no harm.
Despite his nickname correctly conveying his Knight in Shining Armor personality, Paladin on Have Gun — Will Travel dresses in a black outfit that's more along the lines of what a villainous gunfighter would wear in a traditional Western. In fact, a flashback shows that it was originally worn by a gunfighter who Paladin mistakenly thought was a villain and killed him, and he wears the outfit as a form of atonement.
Starting midway through the third season of Babylon 5, the heroes switch from blue-and-brown uniforms to black and silver ones after declaring independence from the increasingly-oppressive Earth Alliance.
The alien enemies are, however, called "Shadows", and they do seem to be quite evil. Of course, both they and their counterparts the Vorlons, who style themselves as shining angelic shapes when out of their encounter suits, are really Ancient Astronauts with Blue and Orange Morality.
Star Trek: Deep Space Nine, and the Star Trek franchise as a whole, got more militaristic black-and-gray uniforms with the only the barely-visible shirts beneath them having the usual colors indicating department. (This after going from mostly-colored uniforms of TNG to just colored shoulders when it began.) Of course Starfleet is still the good guys, though the series was getting Darker and Edgier at this point.
In a TV movie on the making of the Vietnam Memorial several people object to the design because it's made of black marble, which they keep referring to as the color of evil and loss and whatever. They stop doing that when an African American man, in uniform, stands up. Tells of his rank, his years of service, his combat experience and his medals. He then says the next person who calls black evil or the color of loss is going to have to take it outside with him.