This is based on opinion. Please don't list it on a work's trope example list.
Nightmare Fuel / Legacy of Kain
The entire series isn't exactly for kids or the easily spooked, but Soul Reaver in particular was made from stuffed with and basted in this, then cooked to crunchy brown perfection. For a start, there is Melchiah - a massive monstrosity, immortal but constantly rotting, made from sewn-together corpses, lumbering its way across the room, dragging itself toward you by its fingers, which just happen to be severed arms.
Up to the fight with him, you could always escape material enemies by shifting into spirit realm, where they didn't exist, if you lost all your health. This guy? He's there as well, and keeps lumbering towards you...
The Zephonim are spider-like vampires who easily scale walls (for sneaking up on humans) and wrap their victims in spider webbing for later on, to the point where the Silenced Cathedral is full of cocooned corpses...some of which still move.
Zephon himself is even worse. Over the centuries, he devolved into a humongous spider-like creature roughly 30 feet tall, where his entire body has consumed a large room of the cathedral. The first thing he does when he sees you? His face splits apart and he shrieks at you, then later threatens to eat you alive.
In Soul Reaver and Soul Reaver 2, distorted background music plays when in the spectral realm. Though this music isn't necessarily scary, instead of having the usual spectral realm music in Defiance, we're treated to spectral realm ambiance. White noise just above a murmur, peppered with the sobbing, screams, and pleas of lost souls. Choice phrases include: "Somebody help...", "...There is no hope...", "Help me... please... don't do it...", "I don't care anymore, but I'm still so hungry... I died waiting...", a distant horrifying shriek, and of course a mournful chorus that moans Raziel's name.
Blood Omen 2 gives us a call back to the Zephonim in the form of the demons in the canyons; massive green, glowing, pulsing nests of coccooned victims still writhing and moaning as they vainly try to escape. Dialogue that didn't make it into the game suggests that they are being transformed into horrible demonic abominations void of free will...
The Eternal Prison. A place where inmates were being brutally tortured for eternity (which the guards referred to as "peaceful meditation"). You could meet some of those prisoners roaming the corridors aimlessly in bloodied gowns with their eyes sewn shut. Some rooms also contain dismembered, disembowelled human torsos hung on the walls... and they're still alive. The whole place generally consists of dimly lit halls of stone and metal and is chock full of Bizarrchitecture and occasional Alien Geometries.
The sluagh. Their appearance, especially in SR 1, is quite terrifying.
It's a bit low-key compared to the rest, but the Game Over screen in the first game is quite scary: you get treated to a surprisingly realistic view of Kain's skeleton, with his mouth gaping open.
The Elder God: For as long as that creature has existed, there has been no heaven, no hell, no purgatory, just an eternity in the stomach of this betentacled abomination... and it is implied that it may have been around as long as souls have existed. The only reason life is allowed to exist is because this thing wants to maintain a stable food supply.