Good call! And I found out that I was exaggerating! There was only one of 'em.

In Donkey Kong 64, there was a building you could enter (I think in the desert level?) where as soon as you went in, a reticle would appear that would start following you and was accompanied by a very deep gravely voice saying “Get Out!”. 7 y/o me was terrified of that place lol

Nintendo is the Grandmaster of surprise creepy. Just think about it for a while:

Splatoon and Pikmin: In both cases in the backstory, humanity drove itself to extinction. Additionally, Pikmin has several enemies which qualify, such as the Waterwraith.

Splatoon 2 has the Octo expansion where

Kirby: Has quite some real Eldritch abomination bosses.

Mario Galaxy 2:

Super Paper Mario:

; Mimi's transformation sequence; some parts of the Underwhere can be this; Count Bleck's castle and the final boss; also Mimi's extortion house if you think about it, after all what she's doing is basically put everybody into slavery.

Mario Strikers Charged!: As the backstory details, the games got so violent that everybody (except Boo) needs to wear heavy armor and the supportes kept behind an electrified energy field. Playing with a metal soccer ball doesn't help, either. Also has quite some post-apocalyptic vibe: https://www.youtube.com/watch?v=XBinxNwAN5s

The whole plot of Majora's Mask

Earthbound becomes more and more of a mind screw the further you are in the game. And then comes the final boss fight...

But since we are talking about Yoshi in the OP: Just think about the backstory and the implications of Yoshi's Woolly World: Kamek transforms all the Yoshis into Wool to weave them into a super comfy castle for baby Bowser. Bowsers Castle being made out of Yoshis, just let that sink in!

Edit: Here's Mimi's transformation sequence in Super Paper Mario. Has quite an Exorcist vibe:

How dare Nintendo add something unique. Should have been a generic grass level!

Most scary nintendo moment was the announcement of the wii

Agreed. Childlike =/= Childish.

And feeling ashamed to play Mario/Astrobot/whatever because it's in a childlike universe.. Feeling insecure much?

I knew as soon as I read your post what you were talking about: the Cliffside Bayern. That thing scared the ever loving shit out me the first time I ran to edge of that cliff, that it was one of the few moments in gaming where I immediately paused the game, turned it off, and didn't fire up the game for hours/days afterward.

I'm not an outrageous arachnaphobe, but I am when they are the size of a dump truck. If you didn't go find this clip, I would have for you. I remember opening a thread on GameFAQs asking for spoilers on all appearances of large spiders in this game afterward. :p

Also, you aren't totally wrong about the part where TWO of these things come at you at once: in Satorl Marsh, there is a spot on top of a  building where you can trigger a fight against two unique monsters at the same time that are essentially the same thing as that big nasty bastard. Again, it took me days and many, many spoiler videos to work up the nerve to work up the nerve to do that fight.

What about Star Fox? I really wanted to find a GIF of when you first fly into his darkened arena, right into his laughing face, but this will have to do.

River Twygz Bed in Super Paper Mario is kinda creepy too.

It plays when you get to the bottom of a river, if I'm not mistaken.

Pikmin in general, actually. Waterwraith scared the piss out of me the first time I played, definitely the worst enemy. And yes, the whole obvious allusions to humanity's extinction is unsettling. But do you remember the premise of Pikmin 1? That you would suffocate to death if you didn't escape in time? Do you remember

That game is not afraid of death. All those little Pikmin dying horribly, eaten alive, electrocuted, burnt to a crisp, drowned, choking on poison, etc. and their sad little souls just float away looking betrayed. Then there's the final boss of Pikmin 2 where it's implied that

For Kirby, I'd say Marx had to be the creepiest, and Ultimate expanded on him wonderfully adding lots of creepy but totally in character attacks.

For Paper Mario, Mimi definitely deserves mention, but TTYD also gets super dark at times, like when Mario

Or that time

Or how about when Princess Peach

In that same scene,

And then Earthbound is a whole other level of mindfuck at the end. Nothing Nintendo has ever done can touch whatever the fuck that was.