There's quite a number of them. Many of them get delivered by Kumiko, especially if they're video game related.
- During Kazumi's introduction, she mentions that she's from West Osaka, born and raised.
- Kumiko's nickname for Monokuma is Teddie, and her nickname for Minoru is Yoshi.
- Kaito's execution is based on cartoon shorts like those from Walt Disney's era, and involves a dwarf in a mine. The name of the execution itself is a reference to this game on the Snow White DVD.
- During the Chapter 2 investigation, Monokuma mentions that Takara is colder than Macbeth himself.
- Kumiko wonders if something is wrong with Naomi's dreamself when she wakes up one morning in a bad mood.
- Before the trial in Chapter 2, Monokuma appears in front of the students by saying "Hey, hey, hey! It's Monokumaaaa!"
- After coming across Naomi's body in Chapter 3, Kumiko exclaims "Holy Phazon Spores!"
- When the power goes out in Chapter 4, Kumiko shouts out that it's the cause of crows and they need the Legendary Chicken suits.
- In the fourth trial, Kumiko brings up a boy with psychic powers who loves steak.
- Kumiko mentions that Minoru's killer must be a poison type since they used poison to kill him.
- Kumiko shouts out "Objection!" when she disagrees with Takara over the idea that Minoru drank chlorine.
- Kumiko wonders if by playing the archery game she could win a piece of heart.
- Seeing the obstacle course reminds Takara of the sports special with the four stage obstacle course.
- Upon learning that someone among them is a mole, Kumiko says that there's a spy in the base.
- When Takara suggests that Miyako committed suicide by shooting herself, Kumiko doesn't believe it's possible and she won't be convinced by claiming it's an Evoker.
- In Miyako's video will, she mentions that sometimes one must be sacrificed for the good of the many.
- When facing the "ghosts" at the beginning of Chapter 6, Kumiko askes if she's having a bad dream caused by Nightmaren.
- During the final investigation, Kumiko asks if Takara was lead by the power of the Monado to Monokuma's luxury suite.
- After Saemi has been killed and they're all about to leave the simulation, Kumiko says that they'll need more than a Phoenix Down for them to bring back their classmates.