Chapter 10: When Irina starts teaching the kids how to speak in foreign languages, basing her lessons around her experience in seducing foreigners, a female student pictures Jack Sparrow and another student pictures Lara Croft.
Irina's tablet has a list of her personal contacts. One of them looks like Doraemon.
Chapter 12: When wearing a headband for each student showing their weak subjects, Koro-sensei wears a Naruto Headband for a student that's bad in many. The headband makes a comeback before the final exams, but this time many of his "clones" wear it.
Chapter 27: When Irina's master is talking about understanding differences in power, the character chosen to represent this concept in silhouette is a slightly altered but still clearly recognizable Mewtwo.
Chapter 28: Itona's "handler" Shiro wears an anti-Sensei fabric outfit with an upside-down version of Dr. Manhattan's hydrogen symbol.
Chapter 29: When musing over the fact that he has a brother, Koro-sensei briefly envisions himself as Raditz and his brother as Goku from Dragon Ball.
Chapter 47: A rather dopey-looking Tom Nook makes a cameo in a panel depicting Shiro's newest plan to take down Koro-sensei.
Chapter 53: The Science portion of the final exam is depicted as a humanoid giant wearing sturdy armor. When Okuda "defeats" it (solves it perfectly), it happily strips off its armor and awkwardly runs off into the distance, not unlike the Titans from Attack on Titan.
Chapter 58: Koro-sensei claims to be cosplaying Jiro Horikoshi while riding on a hang glider. May be a reference to The Wind Rises, which premiered a few months before this chapter came out.
Chapter 60: Warsman's broken bear claw represents the students's dejection after failing to assassinate Koro-sensei with their most elaborate plan yet.
Chapter 63: The students reason that the virus plaguing the class was orally transmitted. Cue the disturbing imagery of a victim taking a bite out of Anpanman, a visual metaphor for the virus.
In the same chapter, Fuwa fantasizes herself facing off with Ryuk while holding the Death Note.
A short time later, after correctly deducing that Smog was the assassin who poisoned the entire class with the virus, Fuwa mimics Yako Katsuragi'sCatch Phrase by pointing at the culprit and dramatically declaring, "The culprit was you!" She then makes this not-so-subtle statement:
Fuwa: Eh, Jump's mysteries? I dunno, but I hear their paperback edition is out, so maybe I should buy it.
Chapter 66: Yuuji states that his father is a famous TV chairman who constantly gets away with groping the asses of other ladies. The scene is an allusion to Mino Monta, who was caught doing this to a female colleague.
Chapter 67: When forbidding his students from killing people with the real guns they got off the security guards, Koro-sensei wears a Rurouni Kenshin scar.
Chapter 81: The sillhouettes of Lupin III and Zenigata can be seen as Koro-sensei excitedly challenges the class to a game of cops and robbers.
Chapter 82: The students are playing cops and robbers with Karasuma and Koro-sensei. As it describes Koro-sensei letting students constantly escape via bribes and him constantly slacking, it shows him dressed as Kankichi Ryotsu from Kochi Kame, Big Ol' Eyebrows included.