These are what we call the 'YMMV items.' Things that some people find in this work. We call them 'your mileage might vary' because not everyone sees these things in the same way. This starts discussions in the trope lists, a thing we don't want. Please use the discussion page if you'd like to discuss any of these items.
Fridge Brilliance: When you make a Bloody Mary for the captain in chapter 3, you have to use your own blood instead of tomato juice. When the drink arrives to the captain, she calls for the bartender, who took credit for your work, presumably in order to promote him, because she liked the drink. Of course, she liked it - the liquids in human body is what the machine lives on!
Fridge Horror: Look at the things Alicia goes through during all the chapters, but especially chapter 3. Keep in mind that she is pregnant during the whole ordeal. Yikes.
Older Than They Think: A creator version! According to the game's development blog, it was discovered that the cutting edge practice of keeping track of what players do in game to help streamline it was actually done in 1987 by Sierra in Leisure Suit Larry. While disappointed, he still gave props to the man responsible for the idea.
Nightmare Fuel: The reveal of the third chapter. Victor finds himself in the hold surrounded with dead replicas of himself piled around. The machine has been draining them of their live forces.
The appearance the Machine takes on in the various dreams. Large, black, slimy, throbbing tentacles that are literally feeding on the dreams.
Let's not forget the horrifying high-pitched shrieks the machine emits when Victor disables one of its tentacles.
It happens a lot in the game, so you'll most likely get used to it, but the first foray into the dream of another person is really freaky, what with the static, the image of everything around you distorting and a sound that sounds suspiciously like screaming.
Morton's notebook in the fourth chapter implies that he planned to invade the mind of Victor and Alicia's unborn child. In Episode 5, (caution: massive spoiler)this actually happens.
Most of Episode 5, but special mention goes to the organ thief, who is exactly what he sounds like, and the damn eyes.
Squick: When the pixie asks Victor to tickle him, it seems just funny at first, but then the pixie's, uhm, dialogue makes it quite clear that Victor has just been sexually harassed.
Uncanny Valley: All of the characters are this, to a certain extent. It is claymation, after all.