This is based on opinion. Please don't list it on a work's trope example list.
Nightmare Fuel / Xenogears
Though a Teen rated game, it seemed to warrant a Mature ratingnote It actually did get the Japanese equivalent, a D rating; it gave plenty of warning to people who caught the reference to the movie Soylent Green (which would likely be lost on the T rating demographic), nevertheless, one scene in particular occurred in a green factory with a conveyor belt that had dead mutated people dropped on it that then went through giant grinders resembling sink garbage disposals.
And then Elly and Fei realize what they ate in Solaris...
The first scene where we see the mysterious red mech in action , which will later be revealed as being as Weltall-Id, to say that the sheer power and Hopeless Boss Fight at said time is terrifying is an understatement.
Anything to do with the Wels, especially on the second disc, where people start turning into them while "Omen" plays in the background. And it's no small number of people either; everyone who doesn't have Plot Armor (mostNPCs) mutate. It's also implied they don't get better in the game's ending, and are killed along with Deus.
Miang can reincarnate in any woman the moment she dies. As a theoretical, say you're in a town with only two women. She's one of them. You're the other. She gets stabbed and dies. Guess what's going to happen to you?
Let's talk about Zeboim for a minute: prior to the final dungeon, you have the chance to enter a seemingly innoucuous lighthouse, which leads down to the underground and fairly well preserved ruins of a Zeboim city where Fei and Elly lived (and Emeralda was created) in a past life. There are no people aside from Big Joe, and the music, if you can call it that, is just a continual, terrifying gong reminiscent of Silent Hill. You get to explore a whole slew of abandoned buildings, including a television studio, where you learn exactly *how* Zeboim fell: Miang was there too, whispering into the government's ear to trigger a nuclear war. And aside from an optional scene or a visit to Big Joe's shop, the gonging is still happening the whole time.