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.
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.
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
Manga/Dragonball 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 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.
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.
In episode 8 a picture of Ritsuka and Soubi from Loveless appears whilst the class is talking about criticism training.
In this episode around the min. 7:35, Lum can be seen sitting on the moon.
To be specific: 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 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. Coincidentially, the mask in Zoku also happens to look a bit like the Giant's Mask.