Doom (series)/Nightmare Fuel

Classic series

Doom... Demons everywhere. But maybe turning them into Ludicrous Gibs is even scarier.
The face in the HUD also keeps getting bloodier as you take more damage. In some versions, a big hit when low on health makes the head explode.
Daisy! The Doomguy's pet rabbit, with its head severed and impaled bloodily on a stake, as shown at the end of Episode 3 -- and for those who played the original version, this was the end of the game!
The Spider Mastermind. A creepy-ass demon with a brain that's far too big, on a mecha platform with four spiderlike legs and a powerful chaingun that will tear you apart if you're too close.
- And in Doom 2, you find out that Spidey is a mommy -- and her little Arachnotron babies are even worse than her what with their plasma guns.
In Doom 2's map "Dead Simple", when you killed all the mancubi, four walls would come down revealing arachnotrons which proceeded to chase you throughout the map.
Doom 2: at the end of the first major episode (MAP 11), the room containing the master control switch has walls entirely comprised of stitched together corpses.
Despite their relative weakness compared to other monsters, the noise made by former humans as they wander around is quite disconcerting.
The scream the Big Bad of Doom 2 makes when you fire a rocket into the hole in his head that the monsters come from.
There's an example from one of the Final Doom level sets that both qualifies as Nightmare Fuel and makes the developers into Magnificent Bastards. The level starts in a thin hallway with other, shorter ones protruding out from the sides. Walk to the end of one hallway, the wall behind you opens to reveal another hallway, this one filled with monsters. Clear them out, go down the next hallway, sequence repeats. When you go down the third hallway, you've probably caught on by now, so you go down that one backwards... and then the hallway extends and you still get ambushed from behind.
It's bad enough that the red key maze in "Halls of the Damned" (E2M6) is nearly pitch dark, but it gets worse when you realize that it's dotted with Monster Closets, which open with no warning. (Of course one can always grab a nearby pair of lightamp goggles, but that would be no fun.)
The side maze that eventually leads to the chainsaw in "Nuclear Plant" (E1M2) is very dark with fairly erratic lighting, not to mention the unsettling moaning of former humans as they search for you.

Doom 3 and expansions

After Hell invades, go to the bathroom in first part of the game and look in the mirror. A Jump Scare follows as your face momentarily turns demonic and the camera zooms in on it.
Cherubs: Babies with wings and lower bodies of insects, often traveling in swarms and making creepy baby sounds.
The Trites are flesh-coloured spiders the size of sofa cushions with an upside-down human head instead of a body, with eight black eyes to make extra sure you don't get any sleep. They weren't too bad for most of the game but there was a Jump Scare late in the game involving a touch-screen computer and a nice dark compartment behind it for a Trite to hide in.
At one point in the game there was a flight of stairs with a landing covered in blood (the walls, the floor, just drenched with it completely). By this point in the game that seemed like absolutely nothing. But when you walked out onto the landing what appeared to be a face suddenly appeared on that blood covered wall.
The introduction of the Lost Souls. Before you fight them, you hear a woman crying. When you see her, she weakly tells you to help her and she turns around. You get to see her skin greying and her skull forcibly ripped from her head along with her spine.
The scene where bloody baby footsteps appear on the floor, and a ghostly voice implores to "follow me" and "hurry". Eventually, it says "they took my baby", and the screen turns red for a moment as creepy baby cries are heard.

Mods

Less so with the original Doom, but the Aliens custom mod is certainly scary. When you're holding a Pulse Rifle, and there's a dark corridor lit only by a sporadically blinking light, and you hear strange sounds coming from potential corridors in that darkness, willing yourself to press the "forward" key is an exercise in futility.
This is a video of a grown man screaming like a little girl while playing the Doom 2 mod Ghoul's Forest 3. Ghoul's Forest 2 and 3 are quite possibly the most terrifying mods for Doom 2, for that matter. The entire concept is that you're hunted through a dark forest by giant floating super-fast monstrous heads who pop up unexpectedly and kill you in seconds.
- The backstories of the ghouls are creepy: the Big Bad Yurei is the ghost of a pissed-off girl who was abandoned in the Forbidden Forest. The Creeper is the spirit of a baby, the Sjas was a psychotic jester who was executed by the king for a certain joke, the Jitterskull was a Giant warrior, Choke was his demented brother who killed himself. Frostbite (who only appears in the multiplayer mod Ghouls vs. Humans) died of frostbite, so now he can breathe ice and swallow people whole like the Jitterskull.
- The Yurei is an interesting villain, in that she attacks you by making disturbing images pop up and take the entire screen, with predictable results for the player. Yes, that's right, a boss who directly assaults the player.
- The mod is made worse with Icy's addon, which adds a clown; a skull that makes the Jitterskull look like a joke; and a Sjas-like mist cloud that is absolutely relentless. These new ghouls use the terrifying creeper scream. There's also a chance that, instead of the Yurei, the final boss will be the entire cadre of ghouls at once.
The Skulltag Armageddon 2 multiplayer map pack is infamous for the "By Day, By Night" level. It's a map that alternates between day and night. By day? Cheerful demon massacring, upbeat music. By night? The entire map goes dark, the music turns into horrifying loomy ambient, and the monster are... different. And the Eyesores appear. Eyesores are ghouls, just like the ones in The Ghoul's Forest. Imagine a demented, deformed face on spidery legs which runs around like it's on crack, makes weird "kekeke" sounds and can kill you in seconds. And there's an entire crowd of them attacking you all at once.
- The final boss of the map: Clowny. An invisible face which flies around the entire (big and open) final area and pops up suddenly in front of a player for an instant-kill and a Jump Scare. And sometimes it somehow ends up inside the mazelike building you've been in before, forcing the players to brave its silent corridors, expecting the bastard to jump out from behind every corner...
The Happy Time Circus series is the very definition of horror, especially the second one. Wandering through an abandoned ghost town with lots of silence and empty moments, only to have an area completely enveloped by Monster Clowns that you may or may not be able to handle? Oh Crap...
- In the midst of all this, you'll also need to escort "Fluffy" to Clown Hell. Fluffy is a fast-moving, unkillable severed rabbit head that can pass through walls to chew off your face. Good luck!
The Equinox mod, at first, might make you do a double-take when you realize such a well-made mod is from the same guy that made the infamous "nuts.wad". Then, about map 13 or so, you infiltrate an alien space ship. It is incredibly dark, very cramped, the music is creepy, and it is filled to the brim with Arch-Viles.
Brutal Doom is mainly bloody as hell and quite hard, especially on Ultra-Violence mode. But the real nightmare fuel comes with the Spectres. The partial invisibility is gone. Instead, they are completely invisible except for their glowing red eyes. And these things move fast, and are just as intent on nomming you as their pink cousins.
Unloved is the mod that you always wanted to play but hoped no one would ever make: it's a high-res megawad that borrows much of its atmosphere from the Silent Hill series and is exactly as terrifying as it sounds.

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