- To Super Mario Bros. here. The anime version shows up in Episode 15.
- In Episode 2 of the anime, Sasahara can be seen playing with a Game Boy, and later with a Virtual Boy.
- From the same episode: Sometimes I'm a bear, sometimes I'm a be-ar, but my true identity is...
- Episode 4: After putting up the Laying Buddha pose, Mai points her finger up and touches the finger of an alien arm drawn on the blackboard above her.
- In Episode 5, Nakanojou tries to disprove the spiritualist by asking him to summon soap. When the medium does so, he fearfully thought "Is there a person named Soap?" This could be a possible shout out to Soap MacTavish of Modern Warfare, since, for one, both characters sport mohawks.
- In Episode 6 of the anime, a car and married couple from the Game of Life appear.
- Also in Episode 6, Mio delivers Rei's line from Fist of the North Star: "What color is your blood?!"
- When the deer hits the principal, it lands a Street Fighter IV-style Focus Attack.
- Episode 8 references TRON, albeit with an actual bicycle.
- In Episode 10, Sakamoto claims that Jazz legend Miles Davis would be horrified by the Professor and Nano's awful trumpeting.
- In Episode 14 Yuuko kicks her shoe off on top off a car.
- In Episode 16 Mai has a Specialman eraser. In the same episode, during her Unstoppable Rage Mio does Akuma's signature shadow step "Ashura Senkuu" before pulling off a Dragon Screw on Sasahara's Goat.
- In Episode 18, Number 6's last words as he plummets to his death after having failed to entertain Princess Starla are "I have but one regret in my life!" (我が人生に一片の悔い ありいー！, waga jinsei ni ippen no kui...ariiii!), the only changes made to the phrase being the word for "life" used (人生, jinsei instead of 生涯, shougai) and the verb being positive instead of negative.
- The incantation of resurrection that Mai used during the stair climbing game is a password for the first Japanese Dragon Quest (although Mai remembered it wrongly as evidenced by her failure to start her save game later).
- In Episode 20 Sakamoto shouts "Yabba-dabba-doo!".
- The same episode's eyecatch has an angel-thing (?) reading The Sirens Of Titan.
- In Episode 21 Misato and Weboshi each hit Fecchan with a Double Lariat.
- The Episode 21 one above can also double as a Kinnikuman shout-out, as Neptuneman and Big the Budo's move predates the Naruto one, as well as there already being two Kinnikuman shout-outs in the show already. The other shout-out is in Episode 17 on "Like Love" where the boss is doing the Palo Special, made famous by Warsman.
- Also in episode 21, Weboshi has an AC/DC shirt.
- The Professor seems to be a fan of Astro Boy if Nano's adventures in Chapter 178 are anything to go by.
Shout Out / Nichijou