Organized in the order of appearance. Citation(s) would be appreciated.
- Lots of references to SHAFT works:
- Nozomu has a Death Note himself. He uses it to keep track of people he wants to die with him.
- A box of doujin labeled Genshiken appears in the classroom one day, and the table behind Itoshiki-sensei at the Comic Convention turns out to be staffed by Genshiken members as well. In Goku episode one, the Halloween cosplayers include one dressed as Ritsuko Kubel Kettenkrad. And the Tanabata chapter of the manga includes a tanzaku from someone wishing to get into "Shio University" (Genshiken's version of Chuo University).
- Tengen Toppa Gurren Lagann: Has a bunch of references in addition to blackboard gags. These include two separate scenes wherein Nozomu is punched in the face in the exact same manner as Simon punches Rossiu, complete with Art Shift, Punched Across the Room, and the exact same frame-by-frame animations... until Nozomu unexpectedly crashes into a fence headfirst. It Makes Sense in Context; CLAMP, the studio collective who produced this anime, did much of the cleanup animation work on Gurren Lagann. Harumi is seen with Kamina x Simon doujinshi at least twice; once at Zetsubou Sensei's funeral.
- One episode briefly shows the class with desks like from the second Mahou Sensei Negima! anime.
- Another has a set of dolls who bear strong resemblances to various members of Negi's class.
- A Psyche-Lock from Ace Attorney briefly appears.
- Later on, a murder mystery spells out the names of important locations with Ace Attorney's trademark clicking sound.
- As for Neon Genesis Evangelion references, we have Abiru's bandages, that are a mirror flip of Rei's look at her introduction. Nami's birthday party gets a Congratulations scene, like the one Shiji gets in the last episode of the T.V series.
- Harumi poses as Lelouch.
- The opening of the second season is a reference to the Tokyo Grand Guignol's Litchi Hikari Club play.
- In the manga, Itoshiki-sensei seems to be a fan of Edward Gorey.
- Death Note: Light Yagami appears briefly for one page, followed by a confused Itoshiki.
- On the final page of Chapter 15, there's a yonkoma comic strip that's an obvious Affectionate Parody of Sazae-san.
- In Chapter 17 of the manga, a wanted poster for Kira (with a question mark in place of the mugshot) appears.
- There's a chapter in the manga about people saying things they'd never say as jokes (but because it's out of character, it gets taken seriously) — included is Soichiro saying "I'm Kira".
- The class discusses how Nozomu's "confession training" would ruin manga, leading to several imagine spots.Man: Just who is Ki—
Light: I did it.
- In one of the final episodes of the manga, Nozomu is lying in a coffin reading Captain Ersatz versions of the Doraemon, Death Note and Puella Magi Madoka Magica manga.
- Chapter 192 (Combitems), an unnamed character kidnaps Nozomu and chains him in a secret room with random items in a recreation of Saw so she could figure out what he was trying to do with the random items he bought.
- In chapter 162, Harumi imagines Naruto, Kakashi, and Sasuke after hearing about a teacher attacking a defending.
- The blackboards in Itoshiki's classroom regularly sport various messages, quotes, and doodles that reference other bits of pop culture:
- Tengen Toppa Gurren Lagann: "Believe in those who believe in you."
- Azumanga Daioh: "Hang in there, Tomo-chan"
- One Piece: "Zoro x San"
- Code Geass: "ZEROOOOO!" and "I am not Orange!"
- "The monk who leapt through time" is obviously a reference to The Girl Who Leapt Through Time.
- In one of the first episodes: "Screw you guys, I'm going home!"
- When Itoshiki sensei see photos of Matoi and her ex-boyfriends, in one of them she is wearing a cosplay of Dejiko and her boyfriend is seen with a Konata T-Shirt
- Dragon Ball Z: Matoi and Nozomu perform the fusion dance halfway through the Kaere introduction.
- Death Note : While the class is discussing the optimal angle for viewing fireworks, Sensei colapses to the ground, briefly seeing Light Yagami (a direct shout-out to the moment of L's death). Pan back to the students - on the blackboard behind them is written "Death NEET," an obvious reference and pun.
- The bath house story opens with a parody of the Studio Ghibli title card, and has various other references to Spirited Away.
- In the scene where Sensei closes himself in a storage space, he notes things that are found in storage spaces. Among the people referred to are the eponymous character from Osamu Tezuka's manga Ayako and Fujiwara no Sai from Hikaru no Go.
- A picture of Ritsuka and Soubi from Loveless appears whilst the class is talking about criticism training.
- Around the min. 7:35, Lum can be seen sitting on the moon.
- Nozomu is attacked while in the shower by Bruce Lee, Freddy Krueger, and what appears to be a typical Kurosawa character, along with many other characters, in the same style as the famous shower scene from Psycho.
- During Majiru's introduction as Nozomu's 'son', Matoi goes into a rage and wields what appears to be the Flaming Tessaiga.
- When Nozomu is listing famous mistakes, Reinhard and Reuenthal is on the list.
- The practice for "soft" landing is done on an arcade-like machine. On the side in one scene, it reads "Afterburner" from the game series.
- During Ai Kaga's introduction sequence, we can see a random moment where she's sleeping on top of a red dog house, complete with Woodstock (censored by Maedax's face) flying around. In that same introduction sequence, Nozomu, Ai, Chiri and Kafuka are having a snack at a "Ntarbucks Coffee".
- A reference to The iDOLM@STER is made with a girl that looks incredibly similar to Yayoi and a man that claims to produce video game idols.
- Harumi buys a doujinshi whose contents look suspiciously similar to Kuso Miso Technique.
- In the beginning is a scene lifted directly from Jean-Luc Godard's Pierrot le Fou: Nozumo is seen with dynamite wrapped around his head, and following that is a scene where you see the explosion from far away on a cliff.
- The prologue starts out as a bizarre story about cults, but then turns into a parody of Kamen Rider.
- The episode mentions that, at one point, Itoshiki was kidnapped by pirates. We see him on a deck, with the silhouettes of the pirates around him—one of them wearing three swords at his side...
- Around 15:30 there is a brief note that reads "As of today, you have been assigned to Hinamizawa".
- Also Hinamizawa is considered a "double-speak" for massacre.
- In the first minute or so, when our resident Yaoi Fangirl is trying to draw her otp,if you pay attention, she has a poster of Lelouch and Suzaku holding each other and staring into another's eyes.
- Later in the first part, you can see pictures of Mesousa and the cat from the Moe café on Fujiyoshi's pencil holders.
- Mobile Fighter G Gundam, Ultraman, Star Wars, and Neon Genesis Evangelion get referenced in a big way:
- The mask that makes Chiri grow giant is an Ultraman mask. She dispatches the mecha in a shot for shot parallel to Asuka mutilating the MP Eva's. Abiru even hangs a lampshade on it. "Why is she speaking in German?" The last kill is a Mobile Fighter G Gundam reference (though it's called "Bakunetsu Gold Finger," she grasps the head so it's closer to the Shining Finger). Finally, she blows up the Alien spaceship with Ultraman's cross laser thing, stock footage and all.
- That's not all : The way Chiri grows huge is almost exactly the same way Link does when he dons the Giant's Mask in The Legend of Zelda: Majora's Mask. Coincidentally, the mask in Zoku also happens to look a bit like the Giant's Mask.
- Whisper of the Heart: Episode 4 of Zoku, Seiji Amasawa's name appears on the library card.
- Lucky Star: "You're purposely talking about stuff nobody cares about, aren't you? Like how to eat a chocolate cornet! Nobody gives a damn!"
- There is a brief picture of a parody of Eureka Seven, showing a mock Renton and typeZERO.
- Mesousa, Lord Cat and the giant salamander appear briefly in a shopping bag.
- Tengen Toppa Gurren Lagann gets one in the Magical Girl parody, when Nozomu's defeat mirrors Lordgenome's death in the finale.
- At the beginning, Nozomu dons a mask nearly identical to Hei's Reaper mask in Darker Than Black.
- Lucky Star: Bob Ross painting Konata.
- During the Magical Girl opening, Meru is writing out something on her cell phone. The message? Up up, down down, left right left right B A.
- Nozomu's defeat at the end of the sequence is a reference to the end of the Shaman King opening credits.
- Maria, Abiru, and Chiri are wearing the same suits as the main characters of Cat's Eye.
- Ghost in the Shell gets a shout-out when Maria jumps out of the classroom window, holds her hand up as she falls, and vanishes.
- Doctor Slump: Maria mentions that the Prime Minister riding on a "space-age Segway" doesn't look any different than Dr. Mashirito. She even brings out a blurred picture of him!
- This episode features Rena's cleaver.
- The detective parody makes reference to Kosuke Kindaichi, Japan's own Sherlock Holmes with a dandruff problem. In the Blu-Ray special, which features Nozomu as a detective again, he laments that he's not cut out to be a detective because he doesn't have a detective for a grandfather or is a kid with an adult's brain.
- Each of the murders is a Shout-Out to another anime series. One features Kaere/Kaede impaled on a cross with the Lance of Longinus.
- One to Mobile Suit Gundam: A Tanzaku tied a wish to a tree. Its wish? "To become a High Mobility Model!"
- One of the people auditioning for the voice of Meru is Hatsune Miku.
- After the girls begin giving each other face massages, Nozomu notes (in the sarcastic 3rd person) "Sensei, it looks like you're gradually loving girls less and less". Camera pans to Fujiyoshi with a rape smile, who is reading a manga with a picture of Nozomu and Araragi Koyomi◊ from Bakemonogatari on the front cover. The two are kissing passionately.