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.
Anticlimax Boss: Both Final Bosses have pitifully low HP. The Judge only has as much health as the first boss, and you outnumber him four to one. The Batter has even less HP, and you're given an incredibly powerful competence for the battle that can kill him in three hits or less.
The giant flying whales that appear out of nowhere in Zone 2. This BLAM has been the subject of several pieces of fanart.
While running away from Enoch, the hallway suddenly turns into a White Void Room similar to the purified zones. There is absolutely no explanation as to how and why this happened. Considering that the hallways were nightmarish even before this happens, this only adds to the Nightmare Fuel.
Actually running away from Enoch could count as well, especially putting the zany music into consideration.
Most baffling of all is the fish that appears when you step on a certain circular pad in Zone 1. It briefly jumps up, and that's it. The event also only plays once, so you're likely to forget that it even happened. The event itself is even very easily missable, so you're likely to never encounter it.
Not to mention that the fish is the only living thing in the area that's actually in color.
In the Room, you encounter what appears to be either a giant Elsen stuck in the wall or a large, talking mural of one.
On a non-baseball related note, Batter/Wii Fit Trainer are starting to become a thing thanks to the latter's similar pale and featureless appearance, as well as the fact that one of her moves in the new Super Smash Bros. game utilizes several hula-hoops - which fans have joked about resembling the Add-Ons.
All the battle themes, be it boss theme or individual boss battle themes. The whole soundtrack can be listened to here! Note that the page is in French, however.
All of the area music for Zone 2 is very nice. It's appropriately soothing, peaceful, and almost somnolent, which fits Zone 2 perfectly.
One tune in Zone 2, however, is anything but peaceful: Unreasonable Behavior. It plays as you purify the Specters in the residential zone, and it's one of the coolest themes anywhere ever.
Magic Pipe, which is the rather jaunty tune that plays in the Game of the Mortal Fall mini-game in Zone 3 Area 3. It also serves as a contrasting effect towards what awaits you at the bottom.
Front Gate, Enoch's intro theme. An incredibly dark tune, which fits Enoch's overpowering presence and his terrifying reveal about the true role of the Guardians.
Demonic Spiders: The Secretaries, extremely strong and hard to beat enemies that appear in the purified zones, though luckily only in said zones, which are optional and not required to beat the game. Although Secretaries give monstrous amounts of experience when defeated, they tend to show up in groups of 2 or 3 at a time, and do things like hit hard in damage or cast status effects, all of which are very annoying. The most advice one can give you with them is to not directly go to the purified zone immediately after you clear it.
Designated Hero: The player is lead to believe that the Batter is the hero from the very beginning to make the reveal of his more than questionable methods much more jarring, so it's more of an Invoked Trope.
Designated Villain: While the Guardians are all guilty of something, the Queen doesn't seem to do anything. Maybe because she's not actually a villain?
Draco in Leather Pants: All the villains get this treatment in some part or other of the fandom. Especially the Batter.
Dying Dream: A common interpretation of the story is that it's Hugo's.
Ear Worm: Many of the game's songs, the battle themes especially.
The distant yells and whispers in the background when you're in a purified zone. The track that plays in them, Not Safe, is pretty well named.
In the Alma section of Zone 1, riding a pedalo over the meat fountains starts up a very horrid-sounding noise of liquid meat churning. See also Nausea Fuel below.
That gasp Elsens make when they're about to get Burnt. It's just this side of the Uncanny Valley, plus, hearing it means they're about to try and maul you. This gets particularly bad in Zone 3, where the Burnts get nasty.
The crazier Elsens also have a deeper breathing by default, which is just as bad.
Speaking of Zone 3, Endless Hallway. It sounds like something out of Silent Hill when not fighting, and the fight theme itself (heard around 2:56) is Pepper Steak rendered into a painful cacophony, just by making everything percussion.
The Batter's mission to "purify the world" as well as Zacharie's love of money/credits are played up to nearly-obsession levels in Fanon.
Moral Event Horizon: The fight against Hugo, who's only an infant. Arguably also the one against the Critic Burnt crying for help in the Zone 3 subway.
Nausea Fuel: The makers picked a damn realistic sound when they were making the pedalo ride on the meat fountains. Too bad the sound of paddling through a river of meat isn't exactly something that'd stir your appetite.
Overprotective Dad: If his goal was well-intentioned at all, the Batter was most likely trying to be this.
Play the Game, Skip the Story: Inverted. The gameplay is average up through Zone 3 where it starts becoming a lot more frustrating, and almost every boss is a Damage-Sponge Boss with little challenge. However, this is compensated for by the auto option being pretty useful. The real focus of the story is on the gameplay, and to some extent the puzzles.
Ron the Death Eater: The Batter is an interesting and very, very subjective case. Many interpret him as an out-and-out Villain Protagonist and being neglectful at best in his relationship with Hugo and the Queen. Much fanon likes to portray it as flat-out abusive (albeit Hilariously Abusive.) However, part of the evidence fueling these is due to nuance being lost or small translation mistakes due to unfamiliarity - translation 2.0 came out to fix some of these mistakes, and version 2.1 is in the works.
That One Attack: Japhet's "Head Voices" is one of the game's hardest hitters this side of the Secretaries and Sugar.
Speaking of Secretaries, just about anything they throw at you is That One Attack. That is because all of their moves either A) hit like a truck, B) have a high chance to inflict nasty status conditions, or C) both.
The Secretaries look much more detailed than other enemies, which, combined with their already rather unsettling appearance and the places you find them, makes them quite creepy.
There's also one section in The Room where the scenery has much greater detail and colour, calling into question what the real setting of the game is.
What Do You Mean, It's for Kids?: "A nice game for cute children", seen in a piece of official art for The Batter, became an ironic nickname for the game. Interestingly, Bad Batter's sketch and battle sprite is the same pose as in the other picture, but now facing the viewer.
While cases could be made for several characters, poor Hugo is easily the biggest one by far.
The Elsens are an entire race of Woobies. Special mention however goes to the Critic Burnt in the Zone 3 subway, who doesn't fight back and only uses his turns to scream out for help.
The Judge. His beloved brother is killed and he is forced to fight the person he trusted to do good by the world. And if you choose the special ending, he is left with an empty, blank world with only a couple of people left.