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.
Nightmare Fuel / Uncanny Valley: Kusanagi's blank face when Mitsuya wants to kill her is just... scary. Her silver eyes are just ghost-like, and yet, pretty cute at the same time.
Her appearance when she comes out of the ladies' room in the Krakow restaurant is also quite creepy, with her newly slicked back hair and glaringly red lips - she looks more like a doll come to life than a person in that moment. Even Yűichi stares with his mouth open. This could be a reference to another one of the director's films Ghost in the Shell: Innocence.
The videogame contains examples of:
Crowning Music of Awesome: The entire soundtrack qualifies as one, but special mention goes to BGM 5 and all its variants (11, 21, 28 & 29). The composer is Kazuhiro Nakamura.
Narm: Mozume. Despite having a great voice actor (or rather, because of it) his last lines are one of the most hilarious in video games.
The Scrappy: Again, Ukumori because of his 'the weak die in battle' mentality. He's hated even by players, and not just some of the characters.