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 dad? 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.
Complacent Gaming Syndrome: Step One: Get the Phoenix Spear. Step Two: Upgrade it. Step Three: Dive-attack everything in the game to death.
Cult Classic: Sold poorly, likely due to its Misaimed Marketing giving people the impression it was a cheap version of God of War, and initially the only thing most people knew about the game was its weird quirk of having a different protagonist for each version and Kainé being intersex. The few people who did get the game realized it was something entirely different from what marketing suggested, and the game has since built up a pretty glowing reputation as one of the most well-written, unique, and interesting games in the last few years.
Designated Hero: It's revealed that Kainé, unlike Nier, is very well aware of fact that Shades are sentient, however she never drops a hint or tries to stop the merciless slaughter. It's revealed that she's trying to convince herself that they aren't human when Tyrann mocks her numerous times for killing innocent souls, and she yells at him to shut up.
Nier is definitely one, especially considering what the long term repercussions of killing the Shadowlord were. In trying to get back his daughter, he winds up leading both Replicants and Gestalts to their eventual extinction, save Emil.
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.
Magnum Opus: Is widely considered the greatest triumph of both cavia.inc and director Taro Yoko, due to its soul-crushing but gripping writing, amazing soundtrack, and general quirkiness and uniqueness not commonly seen in the genre or most games in general. Amusingly, despite being a Gaiden Game, it's typically considered to be a much better game than the first two Drakengards in just about every aspect, and many also consider it superior to Drakengard 3.
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.
Older Than They Think: Many critics and gamers have praised Spec Ops: The Line for creating an experience where the main protagonist unknowingly kills innocents and which shows the consequences of acting with little understanding of the circumstance, its depressing tone with no clear answers, and its deconstruction of heroism, but this game beat it to the punch two years earlier.
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, namely that the Nier we spent the opening ten minutes playing as transforms into The Shadowlord, and will spent the next 1,312/1,412 years trying to (and failing) to save and reunite with Yonah, only for him to be killed by the Nier we have been playing as for most of the game and his Yonah 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 stepping into bright sunlight flooding from a nearby window a few moments before that.
Killing each of the Shades despite clearly knowing 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 an easy mistake to make since there's a beach right next to the person who gives you the fishing equipment which is where most people would try out fishing instead of slavishly staring at the map to follow the destination marker elsewhere, only for them to end up thinking that they suck too much at the mini game to proceed since all the fish found on the beach next to the fisherman are far too strong to be caught right away.
Superlative Dubbing: Due to its unusual localization process (which led to, among other things, the cutscenes being made with english voice actors in mind as far as mouth flaps go) and excellent voice direction, NieR is widely considered to have one of the best english dubs of any japanese game ever. The dub had such natural-sounding, nuanced performances that most people prefer it over the japanese dub. In particular, Liam O' Brien's performance as Grimoire Weiss is considered some of his best work and the main reason the character was so memorable.
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.
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: Especially after the time skip, 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 JRPG but as a game in general. It's also easily one of the most depressing and oppressive games in recent memory.
Vindicated by History: When it first came out, the game was left to rot on store shelves by non interested gamers and was forgotten. Nowadays it is well known as an amazing game and is considered to be Taro Yoko's best game.
See the Joystiq example in 8.8 above. Initially they slapped the game with a zero only for them later calling one of the best games of the last decade.