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), if more than a bit weird and possessing unquestionably morbid and bizarre tastes.
Similarly, The Munsters are a family of popular Hollywood monsters that act like your average Dom Com type family.
Some of the darker gags in the movie (like the family dumping boiling oil on Christmas carolers) are based on the original Charles Addams strips rather than the tv show, so any charge of Flanderization is probably inaccurate. As well, much like the characters in The Nightmare Before Christmas, they do equally "nasty" things to each other (Wednesday electrocutes her brother for fun, and he seems to enjoy it) and don't seem to suffer any ill effects. Plus, the counselors at the camp really deserved it.
Not only are the Addams family decent people, but they show an extraordinary amount of hospitality and generosity. Gomez, being the philanthropist that he is, regularly gives away surprisingly large sums of money to benefit the community. They've also been known to donate large sums to charities, something they also did in the first movie. Who could ask for better neighbors?
Morticia and Gomez were clearly Happily Married (although the way they expressed affection towards each other could be... odd at times) and got away with public displays of affection at a time when television couples were universally portrayed as sleeping in separate twin beds. (Married television couples, that is.) It tells you something about The Sixties that their most healthy pop culture relationship was the one between a pair of ghouls...
Speaking of ghouls The Munsters were allowed to sleep in the same bed together.
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 the Supernatural episode "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.
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 Doctor in Doctor Who. Before him most Doctors wore very colorful outfits and funny hairdos. The Ninth, played by Christopher Eccleston, wore a black leather jacket and had a very short military-style haircut. Despite his dark appearance, he was 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 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: Crime Scene Investigation, 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 Aliens 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.
Mr. Reese of Person of Interest practically lives in a black suit, but he's very definitely the good guy.