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: Who is June? A heroine justifiably seeking to save herself and give evildoers just desserts, or a villain willing to torture innocents and place them in fear of their lives to correct her own idiocy, possibly with an excessive taste for revenge?
Lotus. She mentions being fired from her cyber-security job and had twins who were abducted and forced to participate in the original Nonary game. How much do you want to bet she was fired for coming close to the truth? Throughout the game, she comes off as, alternatively, selfish and flightly (selfish when she points out that not everyone can live, and flighty when she tells you not to take her seriously), but she's probably using Obfuscating Stupidity. Unless you play the Torture Room, you'd have no idea she has hidden depths — when she talks about psychic powers, she always says it's "just a story." Unless you know she's connected to the first game, it makes no sense, but once you do, it becomes clear she's trying to give Junpei and the rest valuable information without tying it to herself. She's also one of the most competent puzzle-solvers when you work with her, suggesting that she's figured out more than she wants you to know. Badass. As for her noting that only so many of the players can survive to go through the doors? She never said she wasn't willing to sacrifice herself if necessary.
Anti-Climax Boss: Not a boss in the strictest sense, but for all the hyping up the last puzzle got, that was one easy Sudoku.
Unless, like Akane/June, you've never played Sudoku before, and aren't even entirely clear on how it should be played. In which case the "final boss" certainly starts off as frustrating.
Try solving it following the time limit. All the other puzzles only had the titular 9 hours to solve them, save the cabin, and the freezer, which would have taken longer to expire. This is the only puzzle in which Akane had a time limit, and such a short one at that.
Anvilicious: Not obvious at first, but after the game's ending, there is a clear theme running through this entire game: Do not judge things based on your immediate perception. Almost every single thing in this game is devoted to this theme, from the premise and ending down to tiny details such as how you perceive characters and how the puzzles are designed. This whole game is designed to subvert your expectations, and it WILL succeed, spoilers or not. This makes it clear that the developers really wanted people to be able to see things from multiple points of view, and refraining from judgment until you know the facts.
Base Breaker: June. Especially so to fans who've played the sequel.
Snake, as well. According to a poll by Aksys he's the most popular character in the game in the US.
Germans Love David Hasselhoff: Possibly. He's only as high as fourth according to a Japanese poll (although he does remain the most popular male character).
Similar polls show that Clover's the most popular character in the game in Japan, and is second only to her brother in the US.
Esoteric Happy Ending: the upbeat "love conquers all" vibe becomes Fridge Horror when you realize main character Junpei is unable to stop loving the person who effectively tortured innocents to survive and murdered those who wronged her, and who leaves him without a word. Word of God says he chases her unsuccessfully for the rest of his life. To be fair, you can consider it an extremely bizarre form of murder in self-defense. Young Akane needed someone to connect with in the exact same situation. Junpei or Santa wasn't just going to stumble into a Nonary Game. The only future she found where Junpei was in the same proper frame of mind was one where she put him there. Word of God confirms that Junpei would have been willing to save a girl's life had he been asked, just the situation kind of forced it to be involuntary. And deaths surely helped Junpei be in the proper Nonary Game setting to connect with. Considering that these bastards are going to kill Young Akane if she doesn't kidnap them 9 years later and thus save herself...
Also, look at what Junpei does to ensure he enters Door #3 if he insists on taking that path. He certainly understands being a Magnificent Bastard to get what you want, and thus is less likely to hold Akane's actions against her, especially considering she had a much more understandable reason for her actions (read: escaping imminent death and exacting vengeance on the ones who put her through hell) than Junpei did (read: possibly condemning three apparently innocent people to death because he wanted to stay with June).
June's story of the rabbit hutches predicted the deaths of the players, except Ace in Submarine ending, in which they were the rabbits while Junpei is responsible for catching the killer.
In True ending, Ace explained that he only found a mandrake root inside the coffin. In Greek mythology, Mandrake root symbolizes immortality and whoever eats that plant, they went to sleep and never woke up. Other folklore claims that mandrake root links sexual behavior or as a worship to the devil.
Hermes, the Greek god on whom Mercury is based, is a messenger of gods and he often guides travelers to go on safe journey. He's also served as a trickster that's why many Greeks wanted to sacrifice for him. In the Axe and Submarine endings, the mercury symbol at the elevator represents a dead end to the entire group.
According to an interview about the sequel, Chunsoft analyzed that 70% of the viewers for the promotional video are English speakers. In fact, one of the reasons they greenlighted a sequel was because of the International fanbase. Germans love David Hasselhoff indeed!
Hell Is That Noise: Yes, the sound effects. From the cadenced beeping to the ominous creaking of doors.
Except in the True ending, which finishes with the sound of a door closing. In that instance, it's less scary and more like "And that ends this story."
Ho Yay: Some of Snake's dialogue suggests he's kinky and prefers men. Either that, or he's really good at trolling Junpei.
Magnificent Bastard: June, a.k.a. Akane who masterminds the entire plot and shows a considerable ruthless streak in disposing of enemies.
Junpei, usually classified as a Guile Hero, shows that he is capable of Magnificent Bastardry as well; he's just lacking enough opportunities to prove it. So go ahead, give the guy a chance. Insiston takingDoor #3.
Moe: Clover. When she hasn't gone Ax-Crazy, that is. Or even then.
Narm: Junpei in the Safe ending, with his scream of "KAAAAAANNNNNNYYYYYYYYYY!" The pose doesn't help much, either.
There's also the Axe ending which is mostly rightly horrific save the one shot of Junpei's face◊, which just looks unintentionally hilarious.
Seven, in the flashbacks of his rescue of the kids. His facial expressions while he's opening the grate are... amusing, to say the least, in sharp contrast with the situation.
The mostly excruciating Safe ending also provides one of the most inappropriate moments imaginable for a Metal Gear joke to make itself. I guess we can assume that "Snake! Snake! SNAAAAAKE!" would sound better if we could actually hear Junpei's voice.
Player Punch: Snake's (fake) death, if you chose room 5. He is one of the most awesome characters in the game, and one of the most useful.
Snake's (real) death in the Safe ending. It's brutal, and the description (and accompanying sound effect) of Ace kicking Snake's face and upper body is cringe-worthy.
Santa taking June hostage may come as a bit of a shock, especially after he shares a bit of his past and the reason for his cynicism, and after he shows blatant (and apparently genuine) concern for June when she collapses. It's only later that it's revealed that his concern truly was genuine; taking her "hostage" was part of the plan, and his best chance at saving her.
Shipping: Akane and Junpei obviously. There are some moments for Junpei and Clover, but not as much as with Akane. Also Lotus and Seven. The UST is so heavy you can feel it. Lotus/Seven has since been confirmed byWord of God. Also Santa and Clover – when he starts getting all excited about the stairs you're climbing and how they'd be perfect for looking up skirts, he immediately demands that you bring Clover over.
That's probably just for foreshadowing reasons; June is in the boiler room, and yet Santa doesn't invite her up the stairs...