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Nightmare Fuel: Chrono Trigger
That noise that Lavos makes. It's like the audible equivalent of the spelling of "Cthulhu" - if it were real, it would be a Sound That Man Was Not Meant To Hear, and you should be glad this is the best your TV/Nintendo DS speakers can do to replicate it.
It gets better. If one listens closely, they can hear laughter in the background. It's not out of the realm of possibility to consider that Lavos is sentient and enjoys the destruction it's causing. Sleep well!
The Geno Dome has a conveyor belt where a person enters a machine, screams, and what implies to be a Tab emerges from the other end. Even worse in the Japanese version, where it's called the Genocidome, an obvious portmanteau of Genocide and Dome, implying that the machine was specifically built for that purpose.
Magus's Lair in 600 AD. Let's start with the background music, a creepy chord that never lets up, and the laughter every couple of seconds. Add some monsters who look like people you know, whom you know shouldn't be there. They say some relatively innocuous things the first time you see them... then again later after you encounter Ozzie, they add a sinister second phrase before revealing their true forms. Then you find out that the bat that's been following you and flies away just before they change is actually...
This troper isn't even sure that that was laughing...it might have been someone screaming...
Or a mixture of laughing and sobbing/screaming... it's kind of ambiguous, as if the person making the sound is in so much misery and for so long that he's gone insane and, as a result, doesn't even know how to react to it anymore.
Those skeleton Mooks you've fought at various points in this era? At one point in Magus's castle a group of them attacks you while begging you to kill them to free them from the spell controlling them. Worse still, in that castle you meet a bunch of kids and teenagers who also turn into skeletons. Magus wasn't above using child corpses.
The Day of Lavos. Chrono Trigger was originally released in 1995. Back then, a video game showing the End of the World as We Know It happening in 1999 was a very scary thing.
Seeing it in action is nightmare fuel itself in the "bad ending". You see the earth slowly get destroyed from the perspective of its inhabitants at the Day of Lavos, then, followed by that hideous Lavos sound: "But... The future refused to change..."
2300 AD can be pretty scary. A ruined and broken world with no hope, monsters everywhere, and robots set out to scrape the jar's sides, in terms of humans who haven't died already to Lavos or the weather. It's even creepier when the Black Omen starts floating around.
A new player exiting Bangor Dome onto the 2300 AD world map for the first time is in for a shock in general. A barren wasteland, ruins and craters everywhere... but the cherry on top is the freaking world map music. It socks you in the gut immediately with a low piano note, and while the winds are playing a hopeless melody, the percussion lags behind the song's tempo considerably, sounding like the pulley of a lonely flagpole beating against the metal.
And if you wait long enough, many a player has stated that the lightning flash, followed by a low rumbling sound, was a rather unnerving surprise.
The end of the sidequest for Fiona's forest. Lucca gets the chance to relive or alter the point in her past in which her mother's legs become crippled. The sound of the Gate/time warp constantly playing in the background can be disturbing enough, but if you fail, Lucca's mother cries out for one last time before the screen goes black. Two seconds later, you hear Lucca's mother scream. The rest of the sidequest (success or failure) is in complete silence, aside from sound effects.
In your trip into the Manolia Cathedral in 600 A.D, there's one room that you can enter where a naga is off-duty and can be talked to. She only has one line... belching loudly, and then remarking on how the human prisoners also in the room look very tasty. This implies she, and all the other members of the Fiends, have been eating humans, both in the past and quite recently. No wonder most humans hate Fiends!
Fridge Horror: In 2300 AD and the Black Omen, you encounter Lavos Spawn, which would have eventually been cast out into space to find more worlds to consume, just like Earth was. The game never addresses where Lavos (or rather, this Lavos) came from, so how many other planets in the universe have been ravaged by it and/or its kind? There could be dozens, hundreds, or thousands of Lavos' (Lavoses? Lavosi?) hurling around the galaxy right now, each one with enough power to not only destroy whole worlds, but potentially break reality itself.