The dream (or possibly nightmare) Adam has in the trailer, with a group of men in a cathedral during the Renaissance, studying the corpse of a man with dissected arms, who looks exactly like Adam himself. Adam's spirit then rises from the body, grows angel wings and ascends, before they are burned away, Icarus style causing Adam to plummet to the ground. A perfect metaphor for the Transhumanism in Deus Ex, but also incredibly creepy.
The hidden FEMA base in Highland Park. Going down the elevator, seeing floor after floor of mercenary battalions and Boxguards... it's bad enough to think Oh, Crap! at the notion of facing this massive force.
What's going on at Omega Ranch, especially seeing the numerous experimental subjects followed by the refrigerated morgue.
Hyron. Just look at some of the sentences it leaves at the bottom of its official messages, and what it is powered by. Even if you know or suspect what Hyron is already, the final fight against Zhao connected to the Hyron hub takes it to a whole new level. Just listen to the Hyron drones...
The experiments mentioned by the former White Helix employee, of which Adam was the only survivor. Adam was a baby at the time. Turns out Sarif, your boss actually knew about this all the time. So much so that he'd only tell you the truth and send e-mails about Adam's past if you actually win a social battle minigame against him. If you fail the minigame, Sarif will be pissed about you 'focusing on the unnecessary' and tell you to bugger off.
The emails and conversations that make it clear that David Sarif went far beyond what was medically necessary when rebuilding Adam, replacing almost every organic part of Adam's body into machines. Sarif even going so far as to cut off Adam's arms and legs just to add more experimental augmentations, along with everything in the company catalog.
Two of the scariest areas for some were the room in the FEMA facility immediately preceding Barrett's fight and the dissection rooms in Omega Ranch, both of which embodied Nothing Is Scarier. The first has a corridor which, at first glance, appeared to be filled with large crates. But, on closer inspection, it turned out to contain hundreds of inactive Boxguards (read: combat robots eight feet(2.40 meters) high and wide when compacted). None of them activate, but they keep making noises. And in the dissection rooms? All those signs about handling 'subjects' and avoiding contamination, and obviously there's something on the tables, and just as obviously those 'somethings' are not human.
While hardly the scariest thing you'll ever encounter in gaming, Adam's initial steps into the Picus building is incredibly unnerving. Having Adam walk through the pristine but recently evacuated and empty news room of the world's largest media conglomerate, spilt coffee and all, is just plain creepy. Especially when you start reading emails from employees who've been told to pack up and leave in a hurry.
The Missing Link DLC adds a ton of this once you get down to the science labs:
You get to see all of the consequences of being selected for the Hyron system. Random women are taken off the street, incarcerated in an offshore base for no reason, then sent down to a lab for testing. Those who are incompatible for whatever reason (augmentations are one such factor) are killed or shipped off to the Omega Ranch. The compatible ones are placed on an operating table for God knows how long as they have their spines removed and refitted with augmented ones. Many die halfway through this process and could be considered luckier for it. The survivors are shipped off to Panchea to interface with Hyron until they inevitably die from the turmoil (it takes about a year for this to happen). Small wonder that one of the detainees you find in the labs begs for you to kill her.
Aboard the ship you can find dozens and dozens of coffin-like stasis chambers that these poor women are shipped in. Each one has a screen of medical information you can read which breaks down just how much Belltower has dehumanized these people, and that a few of them are marked as risky kidnap-ees because they have wedding rings and someone might want to search for them.
The whole detention camp is one massive helping of Nightmare Fuel. An entire cell block full of prisoners, of which it's all but stated outright that few - if any - have actually done anything wrong. No matter where you go in the main section of the prison, you can hear the prisoners screaming, alternating between righteous indignation at being unjustly detained and sheer terror at the thought of what is happening or might happen to them. On top of the medical experiments, it's made clear that a number of the women have been violated by their Belltower guards. Looking up reveals dozens of more floors just like the three accessible to the player, each with a couple dozen cells... and the prison is rigged so every single one of those cells can be flooded with poison gas in a matter of minutes. And this is one of at least 3 cell blocks - in Detention Camp 5...
The Harvesters gang. Exactly What It Says on the Tin. It's bad enough that muggers in the real world jam a gun in your face and take all of your money. But these guys will rip your arms and legs off so they can sell them or keep them for themselves and leave you bleeding in the street. Granted, they are cybernetic, but if they are linked to your nervous system. They'll cut open your skull to rip out your neural augs. And the person they demonstrate this on? Your pilot, Faridah.
The white room where you find Megan Reed, the room itself seems wrong, but there is also a crash test dummy in the corner that sways slightly, as if breathing. You know the status that dummy has (yes, it has one): dead.
The augmented people on Panchaea who have been affected by the signal. One terrified woman screams at Adam to stay away from her and that he's a monster because he's augmented. At first, she seems like an ungrateful bitch to the highest degree, but her absolute terror is a lot more understandable once she tells you that she saw one of the crazies rip off a guy's arm and beat him to death with it.
Being chased by the crazy augs on Panchaea. The way they run is... unsettling. The noises they make and the way they surround Adam and start attacking them with their bare hands in an attempt to tear him apart are rather unsettling. Depending on how much zombie-like enemies who run and can open doors freak you out, a Pacifist run might be hard to achieve at this point, if only because downing them all in a hail of bullets may just feel like It's the Only Way to Be Sure that they'll stay down. By this point in the game, the player has had time to experience a rich, multidimensional game world and develop an attachment to it. To see this world unexpectedly descend into a zombie outbreak... The effect is arguable stronger than most zombie-based games, where the outbreak has already occurred. Rather than just accept the world as already lost, the player gets to experience the first moments of panic that an actual outbreak might produce.
The "Suicide Apartment" in Hengsha Court Gardens. It's easy to miss, but if you hack the Level 1 security panel and go in, the first thing you see is a pooled bloodstain on the floor, and blood spatters on the wall — just like someone had their brains blown out. Travel to the bedroom, and it looks normal enough — until you notice the large bottle of pills spilled all over the floor. Go into the bathroom, and there's a toaster sitting in the bathtub, along with revolver ammo on the side of the tub. Emails on the apartment's computer imply that the occupant was starting to complain a bit too loudly about Belltower's presence in the building, so it's reasonable to assume the current state of the place is the result of Belltower's half-assed attempt to make the occupant's death look like a suicide.
An in-universe example exists in The Missing Link DLC. To the NPC mooks, you are the Nightmare Fuel. This is especially so if you're going for that elusive Factory Zero achievement because Jensen's resourcefulness and efficiency is all that it takes for him to defeat a well-equipped private army. As one NPC states, "Don't be fooled by the low body count. That just means he's more resourceful."
Speaking of previous Nothing Is Scarier moments, Panchaea before the confrontation with Darrow is all about this. Blood stains are on the wall, corpses are on the floor, and various booby traps are laid everywhere just to prevent other horrors from breaching an area. While the previous levels that were seemingly void of enemies at first had a reasonable, calming reason ("Hey, at least they bothered to evacuated!" in one instance, likely because of a suspicion of you) for being completely deserted, the fact that you know something horrible has happened, and is still happening here is a different sensation. Especially the ambient sound. Just listen, and you'll hear insane rambling coming from seemingly nowhere mixed in between the otherwise fairly silent background. The one time you meet an insane augmentee is from an extremely obvious, barricaded room with only one entrance, and by then you're shuddering at how many others are nearby, just lurking out of vision... And then you actually see hordes of them, everywhere.
If you remember what Bob Page was like in the original Deus Ex, seeing how polite and friendly his e-mails to Tiffany Kavanagh are in The Missing Link is pretty disturbing, especially when he uses emoticons and insists on being called Bob.
The extent of Jaron's augmentations. Over 90% of his body is mechanical which looks like a skinned corpse with alien feet and even his head, the last organic portion of his body, has augments in it. His boss fight involves running around in a museum with other creepy skinless mannequins that he hides with.
The gang that runs the Hung Hua Hotel brothel is implied to force their working girls to get augmentations to control and leash them with the Neuropozene injections augmented people have to take to prevent rejection syndrome. Step out of line and you'll have to deal with painful and often fatal glial tissue buildup.
. Over 90% of his body is mechanical which looks like a skinned corpse with alien feet and even his head, the last organic portion of his body, has augments in it. His boss fight involves running around in a museum with other creepy skinless mannequins that he hides with.