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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: The Screaming Skull
Narm: Giant, transparent skulls flying at the screen just aren't that scary. The Stinger of the MST3K episode is the scene where a skeletal Marian confronts Eric, only for the murderer to smoothly scoop up a stool and throw it at her, sending her component bones flying.
The supremely goofy score at the climax, which Mike laughingly describes as "Bugs Bunny sneaking-up music."
They Wasted a Perfectly Good Plot: The story underlying all of the padding would actually be a pretty good psychological thriller, if it were directed competently, the actors actually acted, and the filler stripped out.
For that matter, the original F. Marion Crawford short story would make a good short film or radio drama.
Fridge Horror: One early riff in the movie has Servo mention to Mike that they're out of embalming fluid. What have they been doing with it and why would they need more?!
Keep Circulating the Tapes: At long last averted. Fans feared the now-copyrighted Gumby short would keep this episode from getting a DVD release, but Shout! Factory has come to the rescue, making it available for the Vol. 31 DVD collection.
Crow: Remember folks, if you die of boredom you do not get a free coffin. Sorry.
No Yay: Partway through the movie, Tom realizes that, at that point, people would be starting to neck instead of being frightened and tries to get Mike to do so. Mike, instead, gets disgusted and tries to shoo Tom.