Ultimate Chimera from Mother 3 (also featured in SSB Brawl and SSB Ultimate) is pretty freaky.

Great examples by everyone, from zelda besides the redead/gibdos and the dead hand i would add the wallmasters, i would play with the volume somewhat low to don't hear the nerving music from the shadow temple and the well, and fuck that made it difficult to know when a wall master was on top of you, because also the ambience was dark, once you know about the shadow how to take them out is easy but the first time they were really creepy taking you out without a chace to respond.

and i think from i coincide with curl-6 everything about the regenerators and the hospital/lab like enviroment they were in was creepy.

let´s wait and see what it is, but despite being the principal enemies sometimes they don't end up as scary as one should expect, from ocarina of time the forest temple looked kinda gloomy and intriguing, but the boss phantom ganon wasn't as scary as it could have been, on the other hand gibdos,redeads, wallmasters, invisible floormasters, and other enemies ended up being more scary, the first two because their damn paralyzing screams, and the others because they were used in a great way alongside a more terrifying enviroment, the well and the shadow temple being not only desinged with a really annoying music, aesthics like dark corridors, torture chambers, endless precipices, were also full of traps and invisble hazzards. 

Let's also wait and see how the E.M.M.I.s and other enemies fare in Metroid Dread, the other games had also some good ones through time, like the SA-X, now the E.M.M.I.s look like that on steroids, Prime 2 had a ton of freaky monsters that could also get more terrifying due to dark posetion/corruption the worst ones for me were the aquatic organisms like the Dark Bloggs, since samus moved so sloppy before the gravity boost and the visor was so cloudy because the water is so full of polution, i knew that if i didn't land precise shots i was as good as dead due to high damage and hi-speed movement of enemies.

Forgot how to imbedd images so Il just go with the Raincoat Killer from Deadly Premonition.

"Right hand" from RE4 was also scary as heck, from the way it stalks you to the fact you're shut in an enclosed environment with it waiting for an elevator to arrive, to the fact that if you don't know what you're doing it can seem unstoppable.

Agreed, all those examples from Ocarina of Time creeped me out as a kid.

My answer will always be Resetti from Animal Crossing.

Deviljho in Monster Hunter Tri was scary as hell when you first got to High Rank, from his mutant T Rex design to the fact he could show up any time to the fact that he could kill you in a single hit before you'd managed to craft a set of high rank armour.

This was probably more awesome than scary in my opinion, absolutely no one asked for it and Nintendo were like "Here is a big Epic mother Dragon to battle!"

It is 100% Gannon. He isn't dead but near dead. The malice has been seeping from his body this whole time. The hand was keeping him pinned down. The jewelry should look familiar to Zelda fans.

Nah it's more Demon/Dark Souls. They are full of Dragons perched on gothic structures and in Demon Souls there is a boss called the Dragon God.