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.
Alternative Character Interpretation: Is Father Nier a good father? He travels to hell and back searching for a way to save Yonah's life, but in doing so he spends so much time away from home that it borders on Parental Abandonment. It's achingly clear that Nier's absence hurts Yonah far more than her illness.
Designated Hero: It's revealed that Kainé, unlike Nier, is very well aware of fact that Shades are sentient, however she never even remotely tries to hint on it or stop merciless slaughter.
She's trying to convince herself that they aren't human. Tyrann mocks her numerous times for killing innocent souls, and she yells at him to shut up.
Fan Dumb/Fandom Heresy: The two versions of Nier, coupled with many people only hearing about the game via poor and sensationalist games journalism, occasionally leads to bizarre statements and accusations being made in comment threads whenever this game is mentioned. A common argument comes from certain NieR Gestalt fans saying that NieR Replicant only exists because the Japanese are so superficial that they won't play a game without a bishounen in it (which in fact is exactly the opposite of the truth), but the dumb can run deeply on both sides. The director having a Viewers Are Morons moment and suggesting in one interview that NieR Replicant might have sold well in France, with the implication that only the French could appreciate Japanese culture, didn't really help....
Fridge Brilliance/Fridge Horror: After finishing the game once, the true extent of the Shades' thoughts, actions and purpose on the world comes to light. And it becomes horrifying due to the actions of the player, who already killed them all.
Also, more immediately, notice that in the end, Yonah was never cured of the Black Scrawl. So she'll either go mad and berserk or die.
Why would Kainé, of all people, turn out to be Endings C and D's True Final Boss? Because it's only the Shadowlord's existence which keeps Gestalts from relapsing. Without it, they lose their sanity and go berserk. Kainé is able to hold on long enough to leave on her own in Endings A and B, before the inevitable happens, but having to acquire all the weapons required to unlock Endings C and D exposed her to far more violence, and the Shade inside her relapses immediately.
Game Breaker: The Phoenix Spear. Without upgrades, it is the best combination of speed and raw attack power, and can one-shot most enemies by the time Nier gets enough money to acquire it, making the rest of the game trivially easy.
The Beastbain, which is sold by the blacksmith in Nier's Village, may count too. It's expensive, but if you're lucky enough, you can get both enough money, and enough items to upgrade it, to make the first part of the game pretty easy.
Nightmare Fuel: A lot, and the more you know about the backstory, the creepier the game gets. Of note is the labyrinth dream in the Forest of Myth, and the paintings in Emil's mansion.
Player Punch: Can't get much worse than the haymaker that is the forced deletion of ALL your save games you've put 30+ hours into in order to see the ending D, complete with each page of Grimoire Weiss being erased one by one, finishing it off by deleting the save files themselves.
It would be more accurately described as Rapid FirePlayer Punches. When seeing a harmless, pretty flower on the title screen reduces even hardcore players to sobbing wrecks...
Although maybe not as strong a punch, learning what happened in the prologue counts, namingly That the Nier we spent the opening ten minutes playing as transforms into The Shadowlord, and will spent the next 1,312 years trying to (and failing) to save and reunite with his daughter, only for him to be killed by the Nier we have been playing as for most of the game and his daughter deciding it's not right to take the current Yonah's body for her own since she keeps crying out to Nier, leaving her body and essentially committing suicide by floating into bright sunlight flooding from a large window nearby a few moments before that.
Killing each one of the Shades despite knowing clearly their tragic backstories.
Stop Helping Me!: Weiss becomes somewhat annoying during some parts of the game, such as the final phase of the battle against Wendy where he might keep repeating the same thing over and over again: he also tends to get annoying during the mandatory part of the fishing minigame by repeating the same hint over and over again instead of asking whether you're even at the right location, which is a possible mistake to make since there's a beach right next to the person who gives you the fishing equipment.
That One Sidequest: The Runaway Son. You have to run about half-way around the world to bring the little bugger back! And then it turns out you were being scammed the whole time. Worse yet, you get no reward for completing it.
Life in the Sands. You have to get 10 pink moonflower seeds. Trouble is you can't find them anywhere, and the only moonflower seeds you can buy are red, gold, and blue. To get pink seeds, you have to hybridize gold and blue moonflower seeds to get indigo seeds, then hybridize those with red seeds to get pink seeds. Oh, did I mention that it takes about 36 real-time hours to be able to harvest these seeds? And that after all that time, there's no guarantee that you'll get the hybrid seeds?
A good number of other less important sidequests also count and some of them seem to be specifically tailored to piss off the player by forcing them to gather a ton of rare items for a ridiculously mundane purpose (such as 10 rare metals just to make a single kitchen knife or 5 sharks for a dish that's ultimately decreed by both the chef and Nier to be better without any), especially considering how much more reasonable the sidequests with actually useful rewards are. Thankfully you don't miss anything by just ignoring them and they largely seem to exist to taunt OCD people about their completion percentage being lower than 100%. The banter you get for each one is nice to hear regardless, even though for most of them it's not worth the trouble.
The Woobie: The main characters could all qualify. In fact, most of the cast could qualify. Hell, the Shades qualify, once you learn what they actually are.
Iron Woobie: Replicant Nier. Both of his parents died before he was ten, but he forbids himself from mourning them in fear of making Yonah sad. Instead, he focused on earning money doing odd jobs in the village, but when Yonah became sick with the Black Scrawl, he couldn't afford her medicine. Nier eventually had to resort to prostitution to provide this (he developed a phobia of people touching his hair from these experiences, which led to him tying it up), but even then he bears it silently, believing that it's for Yonah's sake. Later on, it's even implied that he killed the sex buyer in a Shade-slaying job. Since this is never mentioned in the actual game, you can't even tell from his general positivity that these things even happened.
Stoic Woobie: Nier and Kainé are usually too busy killing things to complain about their problems.
True Artis Angsty: The game was overlooked on the whole, selling poorly and greeted by mixed reviews. However, a few critics and a number of the people in the game's small fanbase consider the game unusually well-written and emotionally powerful, not just for a JPRG but as a game in general. It's also easily one of the most depressing and oppressive games in recent memory.