How to Train Your Dragon: Toothless the dragon is completely black, uses the cover of night to his advantage, his breed is considered the scariest and most dangerous dragon of all, and is on two different occasions referred to as something unholy. The dragon hand-guide describes his breed as an "unholy offspring of lightning and death itself" and Hiccup's father calls him "Devil" in one scene. However, he's also one of the main characters, a "good guy," and freakin' adorable.
The citizens of Halloween Town from The Nightmare Before Christmas, are textbook examples. They even say as much in the opening song (see the quotes page). Even though they're all skeletons, Frankenstein-esque monsters, ghosts, vampires, a Mad Scientist, etc., for the most part they're just fun guys who love a good Halloween. The only one who's really evil is Oogie Boogie - and he isn't exactly popular with the others.
However, they did kidnap Santa Claus, and Lock, Shock and Barrel memorably sang a song about different ways to kill him. Of course, said children work for Oogie Boogie, and Jack hadn't meant for Santa to come to any harm...
Oogie Boogie is actually from a completely different (and very dead) holiday, so he's not really from Halloween Town anyway, as one of the video games reveals.
This is pointed out in Kingdom Hearts, when Sora, Donald, and Goofy wonder why Jack would help them stop the Heartless. Jack explains that while the people of Halloween Town love scaring people, they don't want anyone to actually be hurt, like the Heartless do.
Jack: And one more thing... leave that no account Oogie Boogie OUT OF THIS!
Corpse Bride also plays on this trope. The undead are jovial and friendly both to each other and to mortals, while a lot of the mortals themselves are jerks.
They are also more colorful whereas the mortals appear in what can only be called 'the Tim Burton palette'.
Beetlejuice is yet another example. It features a sympathetic ghost couple who try to scare off a new family that moves into their house with the intent of giving it a massive makeover. The couple meet various other undead people along the way, some hideously disfigured. The dead are all portrayed as eccentric-but-decent people, with the sole exception of the film's eponymous antihero, Betelgeuse, who's really more Chaotic Neutral.
The AnimatedAdaptation is considerably Lighter and Softer, although it also plays into this trope. Lydia is a Perky Goth who enjoys horror movies, insects, rainy days, and other creepy things, and she's a very nice person. Similarly, the Netherworld ranges from freaky to downright bizarre, but very few of the ghosts there are actually malevolent.
His version of Alice in Wonderland has Chessur, an unbelievably unsettling version of the Cheshire Cat, although he is among the good guys. To a lesser extent, the Mad Hatter and the Ugly Cute bear/hyena/reptile like Bandersnatch (originally a bad guy, then changing sides); in the end, the Red Queen's minions also stop being in her side. Yes, that includes the creepy card soldiers.
Meanwhile, the pretty and bland people of Alice's world are almost all shown to be hypocritical, boring, domineering, or shallow.
The White Queen fits in weirdly here, though. Her dominion seems to be dead things, even though she's perfectly nice, so it kind of makes sense.
The ENTIRE moral of Edward Scissorhandsis this. The town starts to judge him by his appearance of being scary and 'monstrous' when in fact he is the most human character in the movie, being caring and downright innocent...
Jacob's Ladder features grotesque... things, that terrorise the protagonist throught the movie. They're actually trying to help him accept his death and ascend to Heaven.
...Unless, of course, you see the very rare removed footage, which pulled a Double Subversion and twisted this back on again, by revealing in a Mind Screw moment, that the "kind psychologist" really IS Dr Caligari.
The Orphanage, the intentions of the other children weren't quite as macabre as originally thought, as they were trying to let her know something crucial.
As if the Hellboy movie hadn't already the eponymous demonic protagonist, the sequel also introduces several magical creatures that, for most part, just want to be left alone. A notable example is the Angel of Death, which is pretty weird and macabre looking, but helps nonetheless.
The vampiric Daywalker Blade is not only dark, he's black.
The Man in Black, from The Princess Bride dresses like a villain, even acts like one in places (more in the book than in the movie), and is eventually identified as the murderous Dread Pirate Roberts - but at the end of the day it's all subterfuge, because he's really the presumed-dead hero Westley.
The titular character of Darkman has a Nightmare Face and always dresses in gloomy black like a classic villain stereotype. Yet, his main goal is to fight the worst city criminals.
Firefox - In this movie, an American pilot steals a super-advanced Soviet fighter jet and is pursued for the last third of the movie across Europe by his Cold War counterpart. The American is in all black, and the Soviet is in almost pure white. (Does it make you the bad guy if you're performing grand theft aero for LIBERTY?)
Ladyhawke. Knight errant Etienne Navarre dresses in all-black armor with red flourishes, and turns into a wolf at night. His lover Isabeau wears a fair amount of black herself; by contrast, both the Big Bad (the Bishop of Aquila) and his Dragon wear white.
Men In Black: They are "Men In Black" but also Earth's "best, last, and only defense against the scum of the universe". Lampshaded in Will Smith's music video.
Good guys dress in black; remember that. In case we ever come face to face and make contact.
The Dark Knight Saga deserves special mention as, probably more than any adaptation, it places a huge emphasis both on just how dark of a character Batman is, but also on how morally good and selfless he is.
In The Beastmaster, Dar encounters a group of bat people who eat their prey by dissolving them with corrosive liquid and drinking them up. However, they are far from evil, in fact getting a Big Damn Heroes at the end by saving the city from The Remnant
The Nega-Scott from Scott Pilgrim vs. The World looks downright evil, red eyes and all. However, he turns out to be a nice guy once Scott confronts him. The two even make plans for brunch.
Jetfire from Transformers: Revenge of The Fallen is an elderly Decepticon-turned-Autobot who turns into a sinister-looking fighter jet, specifically the Lockheed SR-71 Blackbird.
Star Wars has BadAss Mace Windu. His fighting style, Vaapad, focuses on channeling his inner rage and bloodlust into strength and speed. He is able to go berserk on bad guys without losing control and falling to The Dark Side.
Luke Skywalker wears an all-black outfit throughout Return of the Jedi. Just about every depiction of him in the Expanded Universe has him in some variation of that costume.
Zig-zagged in Godzilla (2014). While Godzilla is potentially as dangerous to humanity as the Mutos (if not more so), he also serves as a Destructive Savior. It is notable that Godzilla does not go out of his way to destroy stuff like he usually does.