In Majora's Mask, try going to Great Bay at night. Whole freaking SWARMS of Like Likes; so many that you almost can't walk for fear of being swallowed! And worse? Like Likes in Majora's Mask can move. My reaction was basically "Oh god, so many Like Likes, better be caref— OH GOD WHAT IT'S CHASING ME HOLY CRAP AAAAAAA *tears*".
In Oracle Of Seasons, the place in The Lost Woods where Like-Likes fall from the sky. Where do they come from? Why does there seem to be no limit to their numbers? What would happen if they should break out of the woods and into the other lands?
Also in the Spirit Temple, in that one room when a Like-Like falls from the ceiling. If you just move straight ahead, it'll land right on top of you. Sheesh.
In Ocarina of Time's Ganon's Castle, there's a room where you have to face THREE FUCKING LIKE LIKES in the same room.
Minish Cap one-ups this with the Rupee Likes. Imagine spotting a quarter on the sidewalk, except when you go to pick it up, it turns out to be an anglerfish-style ruse, to get you within eating distance of a giant...um, blob-tube-creature-thing. Man, even having seen Like Likes in 3D, I still cannot grasp their true form.
Phantom Hourglass removes the one thing that makes fighting these things bearable. The boomerang has no effect on them. You have to use your freaking bombs in order to fight these guys. And you have to get up close to attack them. *shudder* Thankfully, remedied in Spirit Tracks.
That's not true. Arrows count as strikes to them, and three strikes count as a kill (I might be mistaken). If you don't want to get close to it (and of course you don't), but don't want to use up your arrows, use your grappling hook. It counts the same (or was it half?) a strike of an arrow. What I usually do is get close to it to pull it up from the ground, then run away, and kill the thing with a few strikes from the hook.
Armos, dear god, Armos. Doesn't help that they look exactly like the standard pushable statues in Ocarina Of Time, and that they frequently can appear in the same room as said statues. Not as scary in other games, mainly because in them they don't make that scary sound every time they come to life.
And in Ocarina of Time they twitch! So an "ordinary" statue will be sitting there, and some glitchy facial twitch (thing) will go off. Eek!
Wallmasters. They fall out of the sky, grab you, and drag you away. Your only warning is the ever growing shadow at your feet that you probably don't notice until it's too late.
Not to mention what they look like. Giant floating disembodied hands. In OoT, they looked like they were rotting, and sometimes they're bigger than you are. Wind Waker takes the cake, though, as the traditional 'fall from the ceiling' formula was mixed up a bit: instead, they come in a strange black-hole like vortex on the floor. Approach it, and a skeletal hand whips out and latches onto your head. You have about 10 seconds to get free before getting sent back to the dungeon's entrance. These monsters, mind, were most often situated in the room just before the final boss room.
The Floormasters were worse. Just as creepy-looking as Wallmasters, only instead of dropping from the ceiling, they would scuttle across the floor like a giant hand-shaped spider, leap at you, latch on, and start draining your health while you struggled to get free. And then when you hit them, they split into three smaller ones that did the same thing but were harder to hit. And if you didn't kill the small ones fast enough, they would grow to full size, meaning that in a worst-case scenario, you could end up with three full-size Floormasters instead of one. And some of them were invisible.
If you hit those three floormasters, and don't kill them, they MULTIPLY TO GIVE YOU NINE FLOORMASTERS.
It's worse than that. You know when you lose track of one of those mini-floormasters, and it latches onto your face and does that weird pulsating thing before detaching and growing to full size...clearly it's not just getting bigger on its own, it's sucking out YOUR life energy for itself.
Keese. Especially early in the game when you don't have a whole lot of health, the way they could swoop down on you out of nowhere with your only warning being the battle music - which was creepy enough on its own!
Keese were even worse when you found out that Din's Fire is useless against them, it just turns them into fire keese.
The cuccos. Sure, they're not technically monsters, but being that my alektorophobia can be definitively traced back to the time I accidentally set off a bomb too close to a cucco, I think they deserve a spot here...
Skultullas. The now-unimpressive graphics of OoT made them bearable, but the ones that appeared in Twilight Princess were FAR too realistically spider-like for this arachnaphobe's liking.
Even the OoT ones could be scary. This troper remembers playing OoT on an emulator when she was 12, and having one fall on her in the Deku Tree. Then, not remembering that Skulltulas have to be attacked from the back, striked from the front once. This troper became completely freaked out when the Skulltula's back with the Skull design turned to face Link, which just to happened to be facing the screen exactly, so it almost seemed as if the Skull broke the fourth wall for a moment.
It's bad enough in Twilight Princess when you can see those hideous skulls on their backs hanging from afar and know you're going to have to face them, but it's worse in places like the Forest Temple where they DROP ON YOU and your nervous system is unprepared and you're too busy screaming to draw your sword. At least when arachnaphobes like this troper see them from afar they can hand the remote control to their brothers until the Skulltulas are gone, but without warning...shudder.
And then there are those times where you either fall into a hole of Skulltulas or fall into a hole with a Skulltula falling ON you... This troper remembers two distinct times... Once when I was trying to kill a Skulltula in the Forest Temple without walking into the pit, but accidently rolled instead, and ended up rolling right into the Skulltula... and another time in the Desert Province, when searching for Heart Pieces, instead, found a hole to be dug by Wolf Link... leading into a den of Skulltula with light only coming from the hole...
The Skultulla House. That is all.
This troper was scared when he was playing this game alone at night, in the Bottom of the Well, a Skulltula appeared right in front of him, he screamed, dropped the pad and ran to his parents' bed just because he's aracnophobe, he didn't play this game for a few months, and finally finished the game after losing his aracnophobia, sadly, the aracnophobia came back and now he can't play Majora's mask
This fellow arachnaphobe would like to point out that, in her experience, she never actually noticed the details on the Twilight Princess Skulltulas' abdomen, and never really had any problem with them— despite running away, howling, if even the tiniest spider approached her in real life. It was only after looking a Skulltula up on one of the wikis and seeing the artwork that she realized how bad they were. It's also possible to miss the head (read: the scary part) of the Ocarina Skulltulas. Which she did. For over a decade. If you really want to,see for yourself.
Dark Link. The ultimate match for you and a reflection of the darkness in your own heart.
Given the right circumstances, Ganon himself can be this. There's the creepy laugh he does at the Game Over screen of Zelda II, beating the stuffing out of Link in Wind Waker while wearing a sadistic smile on his face, removing a sword from his chest in Twilight Princess and just about everything he did in Ocarina of Time.
Peahats. Most games just make them look like strange, flying flowers, but Ocarina of Time's graphics made them look like bizzare alien bladders to this troper. Then, when you get close to them, they fly up and start dispensing tiny versions of themselves like some sort of strange colony creature. They're just plain disturbing.
It Gets Worse. If you engage on in battle during the day (or try to attack it at night) it send out the mini ones. They can (and will) chase you around Hyrule Field as you try in vain to escape them.
The Legend of Zelda (original)
What?? Nobody mentions all the horrors of the ORIGINAL Zelda? That game was almost a stock source of Nightmare Fuel.
To this day, the original Legend of Zelda is the only game in the series where you could hear the boss roaring if you were a room away. It's unsettling walking into a room and suddenly hearing a strange sound effect for the first time (especially when it gets coupled with the next one).
Wizzrobes. There came a point where the difficulty in fighting off several blue Wizzrobes made their mere sight something of nightmare fuel. Especially in a dark room. Old 8-bit sprites like that can look particularly creepy against pure black. Imagine that duck-clown NPC from Superman on NES against blackness. eeeee...
Manhandla, especially if he starts out in the corner and bounces between the two walls, making him appear to shake violently. It isn't helped any by the fact that the picture of him in the manual makes him look one square wide instead of three.
Gleeok. notable as That One Boss, Gleeok did something very unsettling, as well. After you sever a head, the head will continue to live, actually flying around the room like it is possessed by Satan. Oh, and it's on fire.
The battle with Blind in A Link to the Past may have been a homage to Gleeok's demonic intent in the original Zelda. Except this time around, the heads actually spin around, Exorcist style. Not to mention that he first appears disguised as one of the maidens you're supposed to rescue, and doesn't show his true form until you trick him into a patch of light.
All of this is further fueled by the background music for dungeons. It isn't a particularly chilling song so much as a stage setter for a chilling labyrinth, but still, all those things in it...
This becomes assuaged once you play Zelda II. The overworld in the first game was just a small portion of Hyrule in its southern end; all the towns and civilization are actually located farther to the north on the other side of Death Mountain. Ganon likely was incurring his wrath on these areas, but they clearly survived and endured for the second game.