Crash Bandicoot / Nightmare Fuel

Just because these videogames have an excellent palette of colors doesn't mean they can't be potentially creepy at times...

Games with their own pages:

General

The Lab Assistants. It's revealed in Crash Bandicoot 3: Warped that they're all robots, but they look human by Crash standards in the first game. Their only means of attack (apart from standing there) in one level is to run at Crash with arms outstretched, occasionally generating electricity between their hands. It doesn't help that they return in Crash Bandicoot 2: Cortex Strikes Back, some assimilated into Borg-like space warriors, and the only way to beat them is to push them into a fire shield - and their standard cry is eerily cut off as they evaporate.

Emperor Velo's general demeanor is unnerving. The sharp teeth, the sinister stare, his Villainous Breakdown, all serve to establish this entity as a threat, who would clearly destroy the Earth out of spite for losing. Of course, this becomes Nightmare Retardant when his imposing form is revealed as a robotic suit housing an equally tiny and ineffectual alien.

Fahrenheit Frenzy, level 15. It first starts in a volcanic cave with the screen swirling from the heat, with this music playing in the background. It then continues to a canyon with open lava which looks like literal hell, where flying too low will kill Crash with the parts of his helicopter jumping around, which can scare some people. The contrasting green lasers and sprays don't make things better. The second part, mostly factory, is no better either thanks to the hellish red tint. And, of course, there are those X-ray segments.
Py-Ro, the Fire Elemental, when compared to the other elementals, seems the most Ax-Crazy and likely wants Crash to get killed. Doesn't help that Mark Hamill (as in, the same one who is mostly known for voicing the freakin' Joker and who'd later voice another evil fire manipulator) voices him.
- Following suit, the result of Py-Ro empowering Crunch results in the bandicoot becoming a creature made of constantly cooling-and-heating magma that can only growl "DIE" as it chases Crash with a wall of fire and throws flaming boulders at him.
Crunch's body is pushed to its limits when Lo-Lo grants him power. He becomes a living stormcloud wrapped around a gigantic skeleton that begins to show more clearly whenever he takes damage. After being defeated, he explodes into a cascade of giant bones.

That yeti-esque monster gaining on you in the ice levels.
Mega-Mix, the final boss of the game. They're a hulking monstrous fusion of Cortex, N-Gin, Dingodile, and Tiny that furiously charges towards Crash at such a speed that he needs to use the Crash Dash to escape!
- as if that isn't enough, He's Playable in Crash Team Racing Nitro-Fueled. he has a voice of legion and his animations are the same as his fusees... with the added bonus of randomly glitching out before switching personalities. if his dialogue in-game is any indication, all four of the fusees are alive inside mega-mix, and each one is fighting for control of the creature, which is an added level of horror. Mega-Mix is quite possibly the scariest crash bandicoot character yet.

The ski-boarding levels, despite the cheery theme and the fact Crash is just skiing on an ocean, are actually chase levels against a Threatening Shark, and once it's in range to attack you, the music suddenly changes to a modified version of the infamous and terrifying Jaws Shark Attack theme.

Even though the game is remembered for being goofier than the original series, the Dingodile boss fight in the Academy of Evil's boiler room is surprisingly creepy. The arena is darkly lit and only lit by harsh red flames. Dingodile himself is also pretty scary, making only loud grunts and high-pitched squeals as he launches flamethrower attacks at you. The major contributor, however, the soundtrack, which sounds surprisingly intense compared to the other rather breezy songs that make up the rest of the music.
- However Dingodile's actual voice in the cutscene right before the battle is hilarious.
Rusty Walrus can be this. He comes out of nowhere after a battle with N-Gin saying "Aw yummy! Fresh meat for my pot!" and the fact that acts as the Implacable Man since he's immune to Nitro Crates and sealed doors only slows him down makes him more menacing than intended while raising a ton of questions that won't ever be answered.
Evil Crash, in a word, is unsettling. Imagine Crash Bandicoot devoid of any goodness and reduced to a snarling, feral beast driven by bloodlust. Case in point, he violently attacks and devours the Evil Twins after they've been defeated, and is left to presumably attack any and everyone else in his way.
The ending where Cortex gets trapped inside Crash's brain, with only thousands of duplicates of his worst enemy to keep him company.

Even though most of the music in the game is cheerful and fun, some tracks, such as Darkness Imminent and especially Mount Grimly have a much darker, creepier sound to them, with the latter almost sounding out of place due to how unsettling it sounds.