that hallway before you fight the cyborg ninja in metal gear solid 1

In Ocarina of Time, walking out into what was a bustling town to find it ruined and filled with zombies was a real 👀 😨 for me as a kid. Instant raising of the stakes.

Ravenholm in Half life 2

This is gonna sound dumb but I was scared of that Captain Crunch Adventure game when I was a kid. I thought all the animations were extremely uncanny and off-putting. It was on my cousin's computer and I didn't play it much after The Cap'n introduced the game in the cave, because it was just Not Right.

On the trend of Tomb Raider having creepiness, TR2013 definitely did. It even had a scene ripped straight out of The Descent, which itself was paying homage to Apocalypse Now.