The end screen, as seen to the right, scared many at the time especially if if it's their first time seeing it. For those of you who are afraid to click on the link of the alternate image (and with good reason), it's the same end screen as featured, only the words "GAME OVER. RETURN OF GANON" are significantly larger and written in a wilder-looking, slanted text and Ganon himself is even bigger, more hulking and way more menacing than before, the silhouettes of his eyes are more angry-looking and his nostrils also have silhouettes and are flared. Once you see it, you can't un-see it.
Ganon's minions need to kill Link and use his blood as a sacrifice to revive Ganon. No matter where or how you die, if you do they succeed.
Falling into water or lava is unsettling. Link immediately begins sinking as if being pulled in until you can't see him anymore. Then the screen flashes as per the usual death animation, but Link's silhouette is suddenly visible again at the very bottom of the screen, like it is his tomb.
The town of Old Kasuto provides quite an unpleasant shock the first time you enter it. You suspect something's wrong with the place when you see that the town is seemingly deserted, the sky is unusually dark, most buildings are decrepit and partially collapsed, and a slow rendition of the "indoors" music is playing outside. But then you KNOW something's wrong when you suddenly start getting hurt for no reason. You're actually getting swarmed by powerful Moas that you can't see without the Cross artifact.
Link's Shadow is pretty creepy if you're not expecting it. It's also a very hard fight unless you exploit his AI, and without context to the fight you can interpret it as a part of Link that wants Ganon revived.
Yuu Mishozaki's manga has an interesting way to interpret Dark Link, who has a Nightmare Face. Throughout the story, while Link and Zelda are heading to the Palaces, Dark Link is going around Hyrule sullying Link's reputation, corrupting the White Sword into a Dark Sword, until it is finally revealed that Dark Link is really a resurrected Ganon. Link eventually goes into the Great Palace in the hopes of awakening Zelda I, and fights Ganon one last time, who sheds his Dark Link form, transforming into his original kaiju-sized form from the previous manga.