The opening cutscene itself. Aside from falling into Narm territory due to the outdated CGI, even by 1997 standards, it still manages to be creepy for how inhuman and isolated everything feels: Tchernobog's four Chosen are summoned. Once Caleb asks what's the point of their summoning, he possesses a Cultist and proclaims "You Have Failed Me. I disavow you all." After that, the cultist pulls a Slasher Smile before every last pound of flesh sloughs off his skeleton, at which point his monstrous servants close in. Shial drops down to take Gabriel, Cerberus sets Ishmael alight before anyone can notice its presence, and while Caleb and Ophelia are still in shock over that, Cheogh swoops in and drags the latter off to her doom. Tchernobog then disposes of Caleb, imploring him to "consider [his] power in a hollow grave".
Bonus points for the Cabal cultist being possessed by the Tchernobog himself (pictured above), who appears to have his eyes glow white and groaning at the same time, as if he's choking.
Caleb's primary focus upon his resurrection, besides tearing the Cabal and their undead minions limb from limb, is rescuing Ophelia and Gabriel... only to discover that they were both murdered long before he could reach them. Ophelia was crucified in a manner that suggests that she bled out, and Caleb later finds Gabriel webbed-up and hanging in Shial's lair like a slab of meat. Caleb screamingin anguish at the sight of the former really hammers it in.
The prose intro of the Prima guidebook, written from Caleb's perspective, slightly expands on the opening. Caleb's already aware that something is off about this particular meeting, and that his pistol isn't going to do him any good against Tchernobog... In addition, while the game is ambiguous about how long he lay in his grave, the guidebook posits that Caleb was in there for a while. A very long while.
The horrified screams of the Cultists when they die can be jarring the first time. The worst ones sound like they're going through unimaginable torture and play regardless of how you kill them. Albeit, it can verge into Nightmare Retardant if they die to your mundane pitchfork, and it can soon become rather satisfying due to how dangerous and annoying fighting the Cultists is.
The secret level, E1M8: House of Horrors, is true to its name. You open a giant jaw similar to the previous one (this time with a Monster Clown face above it which, superposed over the mouth, gives it a Slasher Smile), then enter a Meat Moss-infested corridor which evokes a giant digestive system: after being "swallowed", you board the River Ride of Terror, a water slide with hanging corpses and creepy laughs coming from all directions, which ends on a trap where you have to dive among piranhas and escape through a Frankenstein's lab torture room. Like the previous level, if you have the CD soundtrack, the Creepy Circus Music is replaced by Fate of the Damned's Redbook version. It's also not clear if the Cabal set this up some time beforehand, or if the House of Horrors was always one of the carnival's "attractions".
Choking Hands, which are the equivalent to Duke Nukem 3D's Protozoid Slimers. These buggers are little enough to be immune to bullet spam, appear suddenly from unexpected places, and when they choke you, you cannot do anything to them except try to pull them off (with your vision darkening, sounds of gasping and your health quickly going down). If you can fight them without getting the heebie-jeebies, you have nerves of steel. If you can kill one with only your pitchfork, you are both utterly fearless and really masterful.
Hell, there are several noises, visions and general stuff that manage to make the game pretty damn scary. Of note is the ominous Domus Durbentia chanting of the voices of Legion in "The Great Temple", apparition on the window at the end of Rest For The Wicked, a ton of stuff in "E2M5: The Haunting"note an eerily large, quiet and dark mansion with several vent holes out of which both Spiders and Hands come crawling, a Hedge Maze way creepier than the one in The Shining, and secret passageways filled with Phantasms, and that's not to mention the Sickening Slaughterhouse - the first building you find in the level and only access much later; it's full of hanging mutilated bodies, disturbingly well-placed blood, and Hands - and the goddamn Creepy Basement and on top of all that the unnerving ghastly moaning without any apparent source in the Ganglion Depths which literally sounds like some unfortunate fellow's soul was trapped in a different plane of existence suffering unspeakable torment. That, and the sense of foreboding you get in any silent level. To boot, if you play the game with CD music on, The Haunting will have "Father Time", easily the creepiest ambient music in the game.
The "Father Time" track starts off as a rather melancholy, atmospheric song, before descending into pure dread.
The Phantasms themselves, thanks to their alarming appearance (imagine a white mini-Grim Reaper with a Slasher Smile) and the way they scream bloody murder non-stop, as well as their propensity for taking you by surprise. As VGJunk puts it, the Phantasms' miserable and hopeless screams sound like a guy whose balls were put in a rat trap.
On E1M2: Wrong Side of the Tracks, you can skip the level exit and go straight into the train tunnel - which results into you walking a long dark hallway in pure silence for a minute, only to get hit by a coming train. This was years before a similar technique was used in games like Silent Hill or SCP-087.
The cruelty of the Cabal is made evident very early on; some of their victims have been nailed to walls and the sides of buildings, seemingly as a warning to Caleb.
Hey, a jukebox! What's it playing? ...The endlessly-looping screams of the damned, apparently.
There's a painting of the Virgin Mary that periodically cycles between her normal state and a skeleton, with rotting stages in between. You'd think Caleb might have something to say about that if you try to examine it, but he doesn't.
There are also severed heads laying on the ground sometimes that do not belong to recently defeated enemies. Look at them long enough and they will look back.
With how stoic and quiet Caleb usually is, it can be somewhat jarring to take a fatal blow and hear him shrieking his lungs out.
Level E2M4: The Overlooked Hotel is a big hotel with a secret passageway in the walls that has no real reason for being there other than that the Cabal likes to watch.
Tchernobog himself is this. A grotesque Eldritch Abomination resembling a rotting corpse with a demonic face, he attacks you by setting you on fire with his magical gaze and launching explosives at you. What's worse is that he's canonically simply a spirit that goes from body to body, so technically it shouldn't even be possible to kill him for good. He can also apparently be summoned simply by talking about him.
is replaced by its even more disturbing variant