The Floormasters are skinny, black hands on arms that pop up when you walk close, latch onto your head, and drag you into a black abyss while making some kind of inhuman screech.
The sound file used for them is recycled from Majora's Mask. Not just the game, but the title artifact itself. Definitely adds to the creepy.
The Redeads. The scary part isn't that they're hard to fight. They're actually rather easy. It's that, if you try to shoot them from afar or from behind, they'll look up and stare into your fucking soul with their empty eyes... before turning back harmlessly to stare into the ground again. Pretty horrifying if you're standing less than two yards behind one of them.
The worst part of the Redeads is that there's just no way to defeat them without getting some kind of terrifying effect. Attack them directly and they let out a chilling scream that will haunt your dreams. Attack them from afar with bombs or arrows and they just recoil from the blast and go back to just sitting there, hunched over. The worst is if you use light to paralyze them first: their normally expressionless faces will twist into expressions of extreme agony, complete with a frowning mouthful of teeth.
In this game, they have one of the freakier screams. Some think it sounds like an elephant, but compared to Ocarina, where they let out a little shriek, in this game they let out a very loud banshee-like wail.
Also, as you can tell from the picture, these Redeads are more cartoonish, but they don't wear the masks that make the N64 Redeads faces look like coconuts.
The worst encounter with them would have to be under your Cabana. You need to go through this mini-dungeon of sorts to get a Triforce Chart. You have to drop into one area and... Two Redeads are waiting for you at the bottom. Dick move game, dick move...
Molgera. Imagine walking into a massive room full of sand. Then you hear a flutey tune play, and sand starts pouring out of the ceiling, and the Triforce disappears under a sea of sand. Then an enormous fleshy worm-thing erupts out of the ground and starts flying around. The worst part is its mouth — the jaws are just whipping around like crazy — and the noise it makes. It sounds like a cross between a donkey braying loudly and an agonized scream. See it here.
It releases little baby versions of itself to fight you that lack the flappy jaw thing, but instead have blank, angry faces and a mouth full of human-like teeth.
On that note, remember Ocarina of Time? How you got to be friends with most of the Kokiri? Well, one of them was chosen to be the Sage, and Molgera ate him!
Sailing around the Great Sea and dealing with most of the enemies isn't a problem, with one exception: The seahats. They're bigger than Link and his boat combined and WILL chase you until you're out of the area, even if you clip their propellers! It's bad enough running into them in clear weather, but it's even more bone-chilling during a storm — day or night.
It doesn't help that unlike most enemies, these things WATCH you the entire time you're at sea. They're constantly facing you as you sail about. When you get onto an island, they pretty much guard it, waiting for you to sail again.
The Big Octos. No matter what, they are always terrifying. If you don't know the secret to finding them, they seem to COME OUT OF NOWHERE AND START SUCKING IN YOUR BOAT. Even if you do figure out where they appear — a large flock of seagulls circle their locations — an intentional sail toward them is full of a mixture of Paranoia Fuel, anxiety, and a generally foreboding feeling. The fact that their markers — the seagulls — go away just before you arrive at their locations makes you none-too-sure of just when the beast will show up and doesn't help the "STOP AND TURN BACK YOU IDIOT" feeling your brain is telling you. And then the whirlpool appears.
For maximum pants-browning, simply take the most direct route possible to Windfall after reaching Greatfish Isle. The Dark Reprise of the sailing theme will have you on edge, the incessant storm will obscure the lone tell-tale sign of its location to you, and you will plow right into it. (Oh, and it's the 12-eyed variety, the biggest of the Big Octos.)
It also hides their other tell-tale sign, being that for some bizarre reason, sailing close to its location immediately brings about a thunderstorm that lasts until you leave or beat the Big Octo. And it starts storming just close enough to the Big Octo that you know it's there, but it's too late to stop yourself.
Like with the Cuccos (chickens) in previous Zelda games, don't mess with the pigs in this game. They will hunt you down! You especially don't want to mess with the giant pig on Outset Island.
At least in this game, the pigs stop after a short time, and they're alone. In Ocarina of Time, attacking the Cuccos will trigger a cutscene of it crowing, and then Cuccos will comes flying at you from literally nowhere. And they don't stop until you die or leave the area.
The Earth Temple is basically this game's Shadow Temple. It's got a huge population of Redeads, Bubbles, Poes, and Stalfos, all of which could probably be considered undead. It's pretty much a huge tomb. Oh, and there's also a huge number of Floormasters. And there's that one room that's full of blue smoke, the stuff that makes you unable to use your weapons, that you have to walk through totally unarmed and sneak past what is basically an army of Floormasters. They can see you perfectly, but you might not see them until they've grabbed a hold of you and pulled you into their portal.
The music from both temples is pretty creepy. The Earth Temple has a slow tune that is occasionally interrupted by what sounds like a lunatic with a wind instrument. The Wind Temple is creepy in a different way. The overtones are an innocent tune reminiscent of the Kokiri, but there's that creepy, constant humming that undermines it.
That sound that starts up around 1:00 is especially creepy.
Sea Octoroks. They tend to appear out of nowhere RIGHT IN FRONT OF YOU with no warning while you are sailing and knock you off your boat, and as you try to get back on your boat, tons of them start popping up all around you surrounding you and firing at you. Not to mention they are also huge and make the screen shake every time they attack, and the music... never go west of Six Eye Reef or near Northern Triangle Island after placing the pearl and getting the treasure...
The places where you get the Triforce Charts in general are horrifying. We have; a holiday home with a flooded basement full of rats, Redeads and claustrobic crawlspaces, a ghost ship, the savage labyrinth, other creepy basements full of enemies, a maze full of Floormasters that chuck you back to the beginning if they grab you... Might be Fridge Brilliance seeing as Link's Triforce piece is the Triforce of Courage.
The sailing music that plays when the Great Sea is cursed. Normally, it's light, upbeat music that makes the lengthy sailing easier, but the cursed theme, which is already pretty bad, is made worse by the constant heavy rain and endless dark skies similar to a dark sky you'd see in a literal nightmare.