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.
Genius Bonus: Several of the stories in the Hall of Records get much funnier if you're familiar with the esotericisms being parodied (like Gnosticism).
There are some jokes (like Willie's "Absalom" crack) that only make sense if you've read the Bible.
Germans Love David Hasselhoff: The Japanese looove Neverhood. So much so the publishers of the Japanese port made their own Gaiden Game for it (without the original creators input or consent).
Not to mention a very large percentage of the fandom is from Poland. There wasn't even a Polish translation of the game. There was a Russian translation, but there's only a few fans from Russia, interestingly.
Tear Jerker: Robot Bil and Willie's Heroic Sacrifice during the battle with the clockwork Beast. There are also stories scattered in the Hall of Records that are like this.