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.
YMMV: I Have No Mouth and I Must Scream
Angst? What Angst?: The boy in Benny's scenario, who never mentions his mother again after learning of her tragic death.
Anti-Climax Boss: The Yellow Rapist in Ellen's scenario. All you have to do is select a dialogue option where Ellen stands up to him, and he falls apart after one strike.
That may have been the point. For all its power, AM does not have the ability to resurrect the dead. It can only create illusions of people, and some of these illusions would just fall apart if attacked. AM thought it could just scare Ellen into submission with an illusion of her rapist, but it did not take into account that she could fight back against her rapist.
Complete Monster: AM is a sentient master-computer who has already wiped out most of the human race before the story even begins, keeping five people alive for 109 years for him to torture physically and psychologically until the end of time. To save time, here's the most horrible of his tortures: trapping Ellen in a virtual reality simulation of the elevator where, years earlier, she was tortured and raped by a psychopath disguised as a repairman- with a simulation of the 'repairman'...
Played with in the endgame. Showing compassion and forgiveness to the Id and Ego, respectively, causes them to tear themselves apart at the inability to understand how their prisoners can empathize with them.
Darkness-Induced Audience Apathy: The story takes place in a nightmarish apocalyptic future where the only five survivors of the human race exist only to be mercilessly tortured by an irredeemably evil omnipotent supercomputer that can never truly be defeated. The entire "quest" that the characters undertake amounts to nothing more than an attempt to make their torture slightly less miserable for a day. It still fails. Bottom line: there isn't a lot of hope in this story, which cheapens the reading experience for some people.
The best ending of the game version, however, ends with AM defeated, 4 of the 5 survivors dead and at peace, and the remainder taking AM's place watching over the system, saying he/she doesn't mind the job and will slowly rebuild humanity using the colony on the moon.Good luck getting it without a walkthrough though.
Esoteric Happy Ending: Ted actually manages to triumph over AM and prove the computer is not the all-powerful god it set itself up as by killing all the other prisoners and freeing them from their torment. A combination of the fact that the price of this is being turned into a helpless jelly-thing to prevent him from ever winning again, and the fact that he's an Unreliable Narrator who's become too cowed by AM to realize he won tends to hide the "happy" part from most readers.
Oh, and there's the fact that for all the Moral Event Horizon AM crossed, it manages to get off with little more than a bruised ego.
Guide Dang It: It's a DOS adventure game from the mid-90s so this could be a given, but many puzzles seem to rely on not missing tiny pixels that represent items that you wouldn't know about. Gorrister and Nimdok's scenarios are particularly bad with this, because you can easily beat their scenarios and go to the endgame without even knowing you missed a step to get their best ending.
The Untwist: Nimdok is a former Nazi. If you know who Dr. Mengele is than you'll figure it out before the intro cutscene is over. Even if you don't the imagery and dialogue in Nimdok's scenario makes it painfully obvious long before Nimdok himself puts 2 and 2 together.
What an Idiot: Ellen's inability to drink the water from the fountain. She says it's because she can't reach, but the fountain is only a few inches deep, and when she finally gets the cup, she has to bend down and scoop the water up the exact same way. Even if she somehow couldn't do that because it's too shallow, it's a fountain. There's a jet of falling water from the top of it.
The Woobie: Who cares about anything bad that they've done. C'mon, how could you not feel sorry for them?