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.
Also the soundtrack. In the last sword fight, the timing of the music is perfect with the choreography, and the chords embody the dramatic tension and climax of the scene. This happens throughout the movie, but here it is most noticeable.
Downer Ending: At the end of the book, the characters are on the run, with indications of trouble ahead and the Prince's forces slowly catching up to them. This is followed by one last 'editor's comment' from Goldman, saying that "life isn't very fair: it's just fairer than death, that's all."
Parodied in the book, with an explanation that a scene with Fezzik and Inigo going on minor quests to save Westley was 'cut' because it seemed like a ripoff of The Wonderful Wizard of Oz, even though the 'original version' came out first. (Unfortunately, the film cut out even a mention of the "deleted scene," which made Fezzik's possession of a holocaust cloak — which he acquires for that scene — seem very out-of-left-field. Many would argue this isn't a bad thing.)
In the film he gets the cloak from Miracle Max.
Vizzini saying "All aboard!". The book notes that this was before trains, but the saying actually comes from carpenters loading lumber, and this was well after carpenters.
The Woobie: Fezzik. Not so much in the movie, but after learning that in the book his parents forced him into wrestling at the age of nine and threatened to leave him forever if he wouldn't fight, you start to feel sorry for him.
Similarly, Inigo. He grew up dirt-poor, and only had his father. Then, a nobleman kills his father for taking offense when the nobleman refuses to pay more than a tenth of the agreed-upon price for the sword he commissioned. Not only that, but in the book, plenty of villagers knew the nobleman murdered Domingo Montoya. They all just let him leave though, because there was no way they could convict him of his crime.