SHAFT's famous quotations on the blackboard and Harumi's fangirlisms are the main culprits, but there are also stuffed toy characters and dances from several shows, as well as split-second references to other anime, games, or general pop culture.
Partial listing of the blackboard shout-outs, subject to change:
Can't remember the exact wording, but once the blackboard featured a shoutout to the guy-on-guy shotaconhentaiBoku No Pico. Seriously.
There's a picture of Pico on the bulletin board that turns into Chico and then Coco later on, during the scene where Kiri offers to show Majiru her swimsuit, no less.
Yet another blackboard gag referenced, of all things, Sylar and Hiro from Heroes.
In Zan there's a caricature of Nozomu in the art style of Bakemonogatari's next episode previews.
Dragon Ball Z: Not a blackboard shoutout, but when Itoshiki is bewailing all the significant historical landmarks that were dwarfed by greater ones, many examples appear in the background; one of them is "Saiyan's strength / Krillin'sstrength"
Matoi and Nozomu perform the fusion dance halfway through episode 3.
And Goku and Vegeta spar in the background while Itoshiki monologues during the non-athletics festival in Zoku.
And then there's Perry's search for the Dragonballs...
Zoku has a whole screenful or two of various characters from other shows, and during the Honey Trap segment included knockoffs of some verypopular series.
Death Note: Light Yagami appears briefly for one page, followed by a confused Itoshiki.
In episode 3 of the anime, 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.
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.
Nozomu has a Death Note himself. He uses it to keep track of people he wants to die with him.
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!" (Zoku Sayonara episode 4)
Not to mention the brief classroom shot with Kagami, Tsukasa and Konata in it - but in Zetsubou Sensei's animation style (Zoku Sayonara episode 9)... or the brief "Chinese bootleg" parody.
Or Bob Ross painting Konata. (Zoku Sayonara episode 7)
In the Hot Springs Episode, Unlucky Channel can be seen behind Kafuka at one point.
What episodes were these in?
In episode 9 of the first series, with Majiru's introduction as Nozomu's 'son', Matoi goes into a rage and wields what appears to be the Flaming Tessaiga.
To be specific: the mask that makes her 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 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.
Speaking of Eva references, Abiru's bandages are a mirror flip of Rei's look at her introduction. Nami's birthday party gets a Congratulations scene.
Later on, a murder mystery spells out the names of important locations with Ace Attorney's trademark clicking sound.
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).
Meru's "death" bed looks suspiciously like the one from Sailor Moon, including her dress.
Nozomu's defeat at the end of the sequence is a reference to the end of the Shaman King opening credits.
In episode 12, 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.
A Zaku tied a wish to a tree. Its wish? "To become a High Mobility Model!"
Part of episode 13 of Zan involves Kiri losing her blanket, and the episode section makes specific reference to the character Linus from Peanuts who is similarly known for an obsession with a blanket.
Episode 12 of the first season has a brief shot of Ai Kaga lying on top of Snoopy's doghouse while a MAEDAX-censored Woodstock flies by.
The fake storybook recap in the second No Man's Land OVA ends with a quick Norio Wakamoto impression.
The bath house story in episode 5 of the first season opens with a parody of the Studio Ghibli title card, and has various other references to Spirited Away.
The opening of the second season is a reference to the Tokyo Grand Guignol's Litchi Hikari Club play.
Macross Frontier: Episode 6 of Zan, as an example of a love triangle.
Whisper of the Heart: Episode 4 of Zoku, Seiji Amasawa's name appears on the library card.
Bokurano: in the same episode as the UNINSTALL blackboard gag, a student writes a letter to the government saying that she's against ZeOOth, as well as GOOdam OO.
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 and Punched Across the Room. In the Magical Girl parody, Nozomu's defeat mirrors Lordgenome's death in the finale. Harumi is seen with Kamina x Simon doujinshi at least twice; once at Zetsubou Sensei's funeral.
In the 5th Zoku episode, there is a brief picture of a parody of Eureka Seven, showing a mock Renton and typeZERO.
Pokémon: "Interesting anime. Boring anime. That is only the selfish perception of people. True home animation quality control managers should try to discuss their favorites."
The 3rd Zoku episode (around 15:30) has a brief note that reads "As of today, you have been assigned to Hinamizawa".
The tenth episode features Rena's cleaver.
At the beginning of Episode 7 Nozomu dons a mask nearly identical to Hei's Reaper mask in Darker than Black.
In season 1, episode 8, 7:35, Lum can be seen sitting on the moon.
In the same episode, 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.
In episode 9 of the first season, when Nozomu is listing famous mistakes, Reinhard and Reuenthal is on the list.
In the manga, Itoshiki-sensei seems to be a fan of Edward Gorey.
At one point in Zan episode 13, there is a picture of KivalabehindMaria.
In the third part of Zan 9, a greyer version of Yusei Fudo (and possibly the MC) is in the train station.
In the episode 3 of Zan, after talking about "switches", Maria reveals that Sensei's 'switch point' is behind his year, while Kafuka tells everybody else about the news. Then Chiri comes, and ends up pushing Sensei's 'Suicide Bomb'Switch point.
In episode 8 of Zoku, Maria, Abiru and Chiri are wearing the same suits as the main characters of Cat's Eye.
Dr. Slump: In episode 9 of Zoku, 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 !
