This is based on opinion. Please don't list it on a work's trope example list.
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.
If you take the time gate to 1999 A.D., you don't hear the normal time gate ambient track. Instead, you get a heartbeat that starts slow and gets quicker every few seconds.
If you go for the Programmer's Ending in a New Game + (using the right telepad immediately when seeing Lucca's device), the inner section of Lavos not only features the heartbeat but an even more disturbing scream that just gets louder and louder until everything else is muffled by it.
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, called "Strains of Insanity" — a creepy chord that never lets up, with a sound that could be laughter, crying, or screaming repeating every couple of seconds.
Add some 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. Instead of the normal battle music, "Strains of Insanity" continues to play while you fight them.
Those skeleton Mook] 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. (And, yes, Stains of Insanity is still playing. Getting to the bosses is worth it just to hear a different song)
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. And 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 broken chimes or the pulley of a lonely flagpole beating against the metal. Or the pendulum of a clock winding down to the last few hours before even what little non-Lavos life remaining on the planet goes extinct.
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.
How about the events at the end of the Ocean Palace where Lavos disintegrates Crono]]! Sure, you can save him later, but still. It comes off as completely unexpected and even with Crono's and Schala'sHeroic Sacrifice, Zeal still is destroyed by Lavos, and not only that but it also causes the Black Omen to be created, on top of flooding most of the planet.
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. She wakes up as the rest of the party sleeps, and the ambient soundtrack of the gate/time warp plays in the background. She wanders into a clearing to find a red time gate. Reliving the worst moment of her life can be disturbing enough, but if you fail to free her from Taban's machine, 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!