After offering to commit suicide with her, Nozumu is stalked by Matoi... who is being stalked by her previous boyfriend who finds her sudden lack of interest in him jarring. And he is being stalked by a woman, who is being stalked by a man, who is being stalked by another woman, who is being stalked by a man who washes her underwear. The two students watching compare him to the Pied Piper of Hamelin, being followed by undesirables.
One of the "in the last volume" nonsense stories, which starts out "Nozomu, a man who loved peace and Stalin..."
The scene at the end of Abiru's introduction in which she forcibly pins a tail on Nozomu and he runs through the street screaming about her being a pervert. Harumi sees him and forces him to wear cat ears.
Nozomu: THIS IS A COMPLETELY DIFFERENT FETISH!!!
The whole "seen it a million times" incident, which includes Harumi realizing that her Yaoi Fangirl tastes aren't shared by the majority and Kafuka producing Komori's "older brother" (a smelly guy wrapped in a blanket).
The incident in which the majority of the girls visit Nozomu at his ancestral home. While Chiri had planned to go, the others basically end up their accidentally, which includes Kiri being kidnapped and some random object put in her place, and Maria lured into a vehicle by a trail of fruit.
The Gag Subbed second episode of Zoku. The whole thing. Commodore Perry goes on a hunt for magical oooo.
The Accidental Marriage episode, the thing itself is pretty funny but the bit where two of the people who are "Good at making eye contact" who were hired (both of whom were guys) to make eye contact and marry Nozomu make eye contact with each other by mistake get shipped out on a minecart, now engaged.
In the "maybe maybe fraud" segment, Nozomu is offered various possible relationships which are said to be able to work which include Nami ("normal love"), Manami ("unfaithful love"), Chie ("adult love"), Kaere ("violent love"), Ikkyu (a raised eyebrow), and Maria ("an acquaintanceship"). Then, Chiri comes and offers "proper love"... and is bluntly rejected. Then of course, she goes Ax-Crazy.
In the All Just a Dream instance, nearly everyone's personalities are reversed, including Nami, who instead of being The Generic Guy and wanting to be special, is odd and wants to be normal. Ultimately, the characters resolve to kill Nozomu to stop the dream from ending, which includes a cackling Nami coming after him with an ax, leading to Nozomu shouting out, "That girl is definitely not normal!"
One of the episodes in the first season has a brief parody of the famous James Bond opening credits, complete with panning shots of Itoshiki and random sliding geometric shapes in the background. In place of the James Bond theme music, is someone going "da-na-na-da-nanana!", and so forth, clearly making it up as they go along. Mock credits list the directors and animators, and Hiroshi Kamiya, Itoshiki's seiyuu, under "music".
You can hear the person doing the "da-na-na-da-nanana!" almost start laughing at one point. This somehow makes it a lot more hilarious.
The sequence in Zoku Sayonara Zetsubou Sensei when everybody starts swapping voice actors.
Episode 7, when they're talking about the 4 panel comics. While discussing the 4 panels, being introduction, development, turning point, and conclusion, Nozomu bursts in and explains there is a secret forbidden 5th panel, "Darkness". the first example used for the 4 panel is
Intro: two boys passing each other in a school hallway
Development: the two boys playing basketball together with sparkles everywhere
Turning point: the boys both punching each other in the face
Conclusion: the boys sleeping together, presumably after sex (it's a yaoi example)
Darkness: a picture of an asterisk with a dark liquid coming out and the word "Hemorrhoids".