- The banter between Weiss and Nier during every fishing quest is hilarious.
- Nier's...unique method of landing sharks and other big fish, specifically yanking them out of the water so hard they go flying.
- When you first meet Weiss and add him to your party, he acts extremely pompous, demands Nier calls him by his full name, finally taunts the shadows that they will meet his thunderous wrath... And after a brief silence, he just lets out a limp "erm", due to the pounding Nier gave to his seal when he saw Yonah trapped behind it causing him to forget all of his spells. Nier is understandably bewildered.
- Nier and Weiss' reactions to Kaine's swearing during the second boss fight in the Aerie.
- Later on, she calls another boss a "shithog", which causes Weiss to protest that it's not even a real word, and Emil also calls the said boss the same thing...despite not even being present when she said it.
- After that boss fight, Nier urges Kaine to live. After she wakes up, Weiss berates her for acting like a coward and not a warrior, that she should live on for her friends, which Nier follows up with "And we are friends now!". Cue a dumbstruck Weiss telling him that was hardly the point of his lecture.
- When Kaine gets captured in the Barren Temple for violating the room's rules. She begins to swear and threaten her capturer with death, not being much more angered than a moment before. "Captured" here means "carried by a cone of light emitted by the kidnapper". The "kidnapper" in question is a levitating cube. Nier and Weiss act barely moved.
- "The Runaway Son" is funny, but mostly because it's quite an impressive bit of game design trolling. What else do you call dashing around the world map to almost every location to find a runaway kid, only to discover (after the fact) that he wants to escape his family's life of crime, and you just tracked him down to help with the family business? Also, you're not going to get paid. It's so completely over-the-top that it spins around from being frustrating and becomes hilarious.
- The Stinger of Ending B combines this with Heartwarming Moments. Emil is just so nonchalant about his Heroic Sacrifice against Popola leaving him as just a head.
- In one sidequest, Nier is sent out to investigate the cause of a child's illness. He finds several berries that appear poisonous, but Kaine tries some, and says they're delicious. Nier tries one, and promptly keels over in pain.
Funny / NieR
Despite the bleak background story, there are many moments in the game that will pull a grin on your face.