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.
Alternative Character Interpretation: Yahtzee implies in 6 Days that 7 Dayswas actually Malcolm's version of the events, and that he was possessed by the Welder and killed the whole crew. He neither confirms nor denies it in the commentary.
The theme is repeated at the climax of 6 Days a Sacrifice, in the scene with Theo walking through Defoe Manor, collecting the items that belong to the welder.
The theme at the beginning and ending of 5 Days a Stranger, as well as the theme at the start of 7 Days a Skeptic. Both taken from RPGMaker 2000 they may well be, but that doesn't make them any less awesome or appropriate for the games.
The introductory theme in 7 Days a Skeptic is a MIDI version of One Man's Dream by Yanni.
Fridge Brilliance: In Notes, the random "insanity effects" responses, particularly the lines and page of "it hurts" over and over, aren't just there to screw with the player. The game is, literally, Trilby's notes. When the game won't respond with anything but "it hurts" or "father why", it's what Trilby is actually writing while he tries to put all of his experiences on the page. He's writing a proper Apocalyptic Log, complete with a sprinkling of Madness Mantra and the account of his own death.
"Funny Aneurysm" Moment / Harsher in Hindsight: In 5 Days, Trilby tricks Simone into believing that he's mentally ill and racked with guilt. While it's all a ruse, his monologue is actually quite frightening, with lines such as "most evenings I cry until I vomit, several times". Flash forward to Trilby's Notes, and he is actually a physical and mental wreck from his experiences in DeFoe Manor.
Idiot Plot: Most the the story wouldn't really work if the characters behaved rationally and worked towards their predefined goals. This is especially true in 7 Days, where no one really knows how to do their job, and the ship itself seems to have been constructed by morons.
A breakdown of what characters were supposed to be doing, and how they failed, is available here.
Narm: The twist ending in 7 Days is a bit lame to begin with, but "I JUST WANTED TO GO INTO SPACE!" would be hilarious even if the context had been better executed.
Nausea Fuel: The alternate hotel in a Layered World. It's covered with blood and gruesome corpses dismembered beyond recognition, one of the worst being bloody handprints being found on the inside of an oven. However, it gets worse when after playing for a while, you notice that most of the guests and staff, including the clerk, have vanished from the normal hotel, and the blood and gore spread across the alternate hotel seems rather...fresh. Word of God states that the alternate hotel is indeed an alternate dimension, and the rest of "our world's" staff just wasn't captured by The Tall Man... that's All There in the Manual.
And before that, Taylor's room in 7 Days. When you finally get in, it turns out he's been butchering the crew and stitching the parts together into a new body for John DeFoe. The "leftovers" are everywhere, including the meganekko's severed head, still wearing her glasses, lying on a table.
And all of that is still nothing compared to the horrors the main character in The Expedition experiences, when he gets trapped in the body of Chzo.
Trilby's Notes, in many respects. If you've played it, a handy way to avoid sleeping is to turn the lights off and listen to the music track that plays in the alternate hotel.
So Bad, It's Good: No, don't worry, not the games themselves. The Let's Play of the Mythos had various challenges and mini-contests between some of the episodes. One was to find the worst fan-made work for the series. Yahtzee himself participated, having found a community college made film based on 5 Days A Stranger. It's about as cheesy and poorly acted as you'd expect, they can't pronounce "Trilby" correctly, for one thing.