Please don't list this on a work's page as a trope. Examples can go on the work's YMMV tab.
Nightmare Fuel: The Legend of Zelda: A Link to the Past
Ahh! Kill It with Fire! note Literally. The only way to go inside is to burn the mouth with the fire rod.
The manual describes how Ganon got his hands on the Triforce, corrupted the Golden Land, and became a beast.
After vanquishing his own followers, the leader stood triumphant before the Triforce and grasped it with his blood-stained hands. He heard a whispered voice: "If thou hast a strong desire or dream, wish for it..." And in reply, the roaring laughter of the brigand leader echoed across time and space and even reached the far-off land of Hyrule.
The basic soldiers have very good AI and will actively chase you if they see or hear you. They can also hide in shrubs and only appear when you cut one, or disguise themselves as bushes to snipe you with crossbow bolts.
Link is framed for Zelda's kidnapping at the start of the game, making Kakariko Village an unsafe place to be. If citizens see you, they'll sic guards on you until you leave the screen or kill the guards.
The music in the Dark World before you obtain the moon pearl. Try accessing the map screen and you see a lifeless, gloomy, twisted version of Hyrule laid out while that music is playing.
THE GORIYAS. In this game, they're fairly large, they mirror your moves (the red ones also shoot arrows), and there are black hollows where their eyes should be.
Here's some Fridge Horror: The most common enemies you fight in the Light World are brainwashed human soldiers, members of Hyrule's military. You're killing members of your own side whose minds have been enslaved by their enemy. And imagine what things will be like after Agahnim and Ganon have been defeated for the families of the brainwashed soldiers.
It gets worse when you talk to one of the soldiers around the castle, before you get to the ones that attack you, who says that everybody around him seems to be turning evil, and surrenders to the likelihood that whatever is doing that will get him soon.
It's implied that the World-Healing Wave at the end undoes this, as the King and Link's Uncle are shown alive and well at the end - so why not the random innocent mooks you killed?
Agahnim is probably one of the most competent Zelda villains; he kills the King and apparently vaporizes the maidens, including Zelda—the latter right before Link's eyes. When he's defeated the first time, he transports Link to the Dark World.
In the opening to the game, you can see the Hyrule King deader than dead (meaning only his clothes and bones are left).
in the GBA release you're forced to watch the intro everytime you start a new file, whereas in the original SNES version it only came up as long as you didn't press start on the title screen.
The many thieves lurking in both the Lost Woods of the Light World and the Skeleton Forest of the Dark World. They follow you constantly (unless you fake them out and leave them obstructed by a tree stump of whatever), if you do encounter them directly, they bump into you without warning and make off with your hard-earned goodies(!) like rupees and bombs before you can even grab them back for yourself, you CANNOT kill them or even wound them, and both versions by themselves are pretty creepy in their own right. Since animals replace people in the latter, when you first see it, you think nothing of a random fox until it approaches you and the former has a permanent scowl on his face and has white triangles where his eyes should be. Yikes.
If you exploit some glitches to battle and defeat Agahnim early in the game before you get the Magic Mirror or Moon Pearl (as mentioned under Unwinnable by Insanity), you get transported into the Dark World, where you get transformed into Bunny Link and can do absolutely nothing beyond wandering around helplessly until you eventually get killed. In addition to being a scary enough concept in itself — not helped by the somber "Bunny Link" theme playing as he gets pelted by spears and bombs from the assorted enemies — the horror of the situation is turned Up to Eleven when you realize this was the fate of everyone who wandered into a magical transporter or got zapped into the Dark World by Agahnim.
This is the first game in the series where Ganon has the entire Triforce.