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.
Holy Shit Quotient: What April finds when she finally enters through the mystery door, the one you can see back in the first chapter but was locked. It is the old lady who is narrating April's story in the beginning of the game. The nature of this encounter still is matter of speculation for the fans until this day.
The majority of the character animations looked awkward and uncanny valley-ish even back when it was new. And they have not aged well... this spells doom for any attempts to pull off dramatic scenes. It's just as well it knows not to take itself too seriously, eh?
The dark silhouette of young April during her second trial looks distractingly similar to the titular Mysterious Alien Creature from Mac and Me...
Seinfeld Is Unfunny: Different example - as one may notice from the picture of the cover box, the game is rated "M", most likely due to the innuendo that Burns and April throw around and the occasional swear word thrown around in Stark or April's dialogue. However, 15 years later, it's significantly tamer than what you've come to expect from a game that's rated M.