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.
Depending on the choice of the gender of the players, the yandere groom/bride in the chapel part of the game which their other half got killed, are none other than Ikuta and his wife Tomoka. If you follow the patterns of the later chapters of the game, it's like Asahi was telling you her interpretation of what her parents could have felt when in case of Ikuta's, his wife died or, well, the 'revenge' for her mom to him after not coming home the night she got murdered.
Odaka orders a LOT of holy water to be brought the day the main character goes to his appartment. According to the NPCs of the first village of the game, the water in there cures whatever sickness. Just think about it, Odaka gets sick during the week he was playing the game, he couldn't get past the first location, and since he would also have been bothered by the Regrets or Asahi herself... the game made him go obsessed or went nuts, and believed that the characters were telling him the truth, so it could have been the way to "exorcise" himself if he made it through the final day or of the ghosts that were pestering him, but didn't make it and ended drowned inside the game itself.
The good ending. When the game ends, you get a final email on your TS from Asahi with a single short message: "Thank you."
The fact that Mr. Ikuta, the game's creator, named the game "Load (Road) to Sunrise", after his daughter Asahi whose name loosely translates to "sunrise".
Hell Is That Noise: The background music starts as reminiscent of Dragon Quest, then gets increasingly glitchy until it's nothing but dissonant ear rape.
In the Gainax Ending of NNG Me, you listen 'something' talking to you. While in the game is notorious how you receive help from Prof. Ohyama in your TS and it sounds like when talking to an RPG character (for obvious reasons)... this 'thing' speaks to you as it is a splash of mud water. Horrifying splash of mud water.
The game as a whole, but especially the murderer, Yutani Shin, on the fifth level. The whole screen is tinged in red and he is a persistent chaser. You play as Asahi who runs throughout the house trying to escape only to find him in every room she goes into. This may very well be the most frightening moment in the entire game.
Another noticeable one is at the end of Chapter 6. Your university professor Ohyama has been a constant ally who finally falls victim to the game. When you meet his ghost, he actually starts to run at you.
The Woobie: Poor Mr. Ikuta. All he wanted was to create a game dedicated to his family. His daughter Asahi hates him for spending so much time on it, and he ends up losing his wife and daughter. When you investigate the old Ikuta residence, you discover a disheveled white-haired Mr. Ikuta huddled in the closet in a catatonic state, clutching his daughter's diary.
Woolseyism: When you view the cursed game's ending sequence, the credits suddenly stop and the first characters of the on-screen names turn red, which spells out "I won't forgive you". In the fan translation patch, this is changed so the words "YOU DIE" are formed by taking letters from "Yutani", "sound", and "director".