Himeko's last name is Onizuka, another show about a former delinquent...
who became a teacher. Come back when the Birdman arc happens and you find out that Himeko's dream is to become a teacher. Another ex-delinquent, which last name is Onizuka wants to become a teacher.
Then there are several to Gintama, mostly because not only Shinohara was Sorachi's former assitant, but they ended as friends in real life.
Kondo and the Student Council President look alike.
Bossun and Tsubaki have a rivalry similar to Gintoki and Hijikata.
In ch 72, Switch reccomends Shinzou to use Gintoki's clothes. More even funnier in the anime since Switch (Tomokazu Sugita) uses Gin's tone of voice and the others lampshade it.
In episode 3 Bossun asks Himeko if she can master Bankai. The episode/chapter where Himeko replaces her hockey-stick has Bossun suggest that she name it 'like a zanpakuto'.
Switch apparently introduces himself and states his favorite Espada (Aaroniero Arruruerie) in the manga and Vizard (Kensei Muguruma) in the anime. The last is also a shout out to his seiyuu as well, since he also previously voiced him.
In episode 5 the way Yuuki enters the SKET Dan club room is an obvious reference to the Ringu (especially as the eyecatch is the same but with a the background changed to TV static. Given her being that ghostly in appearance, it fits her character as well.
Episode 10 starts with a hilariously accurate parody of Kimi ni Todoke at the beginning. In the manga, the original chapter was parodying Ichigo 100%.
Episode 15 introduces us a teacher who looks like Jason with J-son as his nickname, for all things. Later, Date writes a spiral which Switch thinks he is referring to Uzumaki but Date was in reality meaning Naruto. Switch can also be seen playing a game based on Katekyo Hitman Reborn!.
From the manga equivalence of Dante's first appearance, Switch mentions that he, using a symbol with furigana, reminds him of the Majin Tantei Nougami Neuro's chapter titles.
Episode 19/Chapter 48 has Bossun getting his hair cut like Goku from Dragon Ball and Switch channels Cell and he even imitates his seiyuu (Being said, this is not the first and only time Sugita has imitated Wakamoto's voice.)
A later episode has Shinzou trying to pick out casual clothes with Switch making him dress up like Vegeta, hair and all. Piccolo's clothes are also seen in there as well.
Switch's nickname around the web (Vivage City, Momoka's blog, sometimes even Twitter) is Porunga.
When Koma hits Bossun with her ''Koma's cannon' in chapter 95, Bossun ends up with a rather familiar death stance in the ground...
In episode 15, Dante mentions Makankosappo (Piccolo's Special Beam Cannon) during the second eyecatch.
In episode 20, Himeko briefly turns into Eiji (complete with weird hair and pencil) from Bakuman。.
In chapter 72, Shinzou is dressed AND acting as Eiji, too. The Next Episode Preview of episode 30, has him talking about his dreams, similar animation, and even an Captain Ersatz for Azuki.
Roman's introduction to her guide to how to draw a manga, in chapter 115, mentions the series' name to look up with some terms as for example, what a name is.
Roman also makes a promise as the one of Mashiro and Miho, in episode 9.
In the first chapter, when Teppei is with the Sket dan, Bossun gives him the name of Penki Kurai-man, which Switch pronounces it like P.Cry-man and then Himeko lampshades this in a tsukomi reclaim.
Chapter 129 has one to Harry Potter, with the group getting an owl, that at some extents it also gets lampshaded by the group, given the awkward silence they have when they rescue it in the first place.
Episode 29 has one with Switch saying ''Something has disappeared, like Haruhi(to those unfamiliar, Switch's voice actor was Kyon).
Episode 30 has a shout out to, of all things, Special Duty Combat Unit Shinesman. One of the members of the Slender sentai team is "sepia," one of the same colors of the Shinesman. Himeko calls sepia a lame color, referencing a Running Gag in Shinesman of people making fun of their colors.
The game system in episode 39/chapter 91 resembles the Famicom (mostly because it is a Chinese Bootleg, made by Master Huang himself). The video game the characters play is a bizarre cross between Super Mario Bros. (with even suspicious similar protagonists' names) and Dragon Quest (the random enemies battles). Additionally, the dialogue over the first eyecatch of the anime was one of the slogans from the advertisements for the game MOTHER.
Speaking of the Mario Bros, two waaay too similar characters appear in the Sports School Festival on Kaimei... Suwa Mario-kun and Luigi-kun... who's only time to shine is in there (supposed to be pros at obstacle courses).
They are many shout outs to JoJo's Bizarre Adventure from Dio's 'WRYYYYYYY' vampire cry in episode 22/chapter 40, to a Stand in chapter 55, inconciously convocated by Roman in her how to draw manga guide... to the ridicously funny pose that Bossun ends up in ch 220.
Roman's 'stand' in her shoujo manga is named Lover Soul in the same nature that Araki does normally in his series. It's probably referring to J-music group, Judy And Mary, too.
In the Next Episode Preview of episode 6, Switch mentions Yare Yare Daze, in Jotaro Kujo's way of saying it. It's funny, that later Tomokazu Sugita would have voiced another Joestar as well, Joseph Joestar who is the grandfather of Jotaro later in Part 3: Stardust Crusaders in the TV Animation from 2012.
The phrase of 'Yare Yare Daze'' is also played on a cardboard in a record/DVD store in episode 43.
In chapter 220, Switch goes to see a seiyuu by the name of Marina Onoue, a play on Momoka's VA, Marina Inoue.
Several mentions of Kinnikuman are also in there, like the time they were playing Hyperion with a figurine that looked so much from the original protagonist of the series, and mentions around here and there of the Kinniku Buster.
Other references to Katekyo Hitman Reborn! are made especially in the anime with Gokudera (named as Gowadera) appearing in the cover of the Shonen Jump when the manga based on the Student Council surfaces. He also appears on Dante's flashback in episode 15.
In the crossover chapter/episode with Gintama, Shinpachi refers to the series, when changing two characters in the name of a manga series as Ritekyo Hitman CABORN!.
The plot of the Ninja World's Alternate Universe chapter is based mostly on it. With such references as Bossun's saying '-ttebayo' and Switch's changing clothes to make him look cooler (like a Genin).
Bossun, at the end of the mini-arc of the Fake Fortune Teller, he mentions 'dattebayo'.
In the full Biscuit Dance chapter, when Agata is suggesting for a play, Dante mentions of a 'Masked Shitobi' (Kakashi).
Kiri's dad thinks that Sasuke sounds much as a ninja name... sadly, Tsubaki really sucks at learning ninja skills (though in defense, it couldn't be just a reference to Naruto, Sasuke is indeed used for many ninja characters, one in mind is the servant of Kuno Tatewaki, who was an exclusive character for the anime series of Ranma ½.
Roman, being almost the 'Queen of Old-School Shoujo Manga' in Kaimei, often refers to old shoujo works such as Candy Candy ("My prince of the Hill" which Switch refers it to be from the source material of Gyarando Gyarando)), she channels sometimes as one of the characters in Glass Mask.
The first appeareance of Enta Hinohara in episode 09 is that misleading in the anime since he looked like a certain God of Manga... covered in light.
Speaking of whom, the shonen manga club's assesor. Kezuka, is a race-flipped reference to him as well.
Mentions of Doraemon are also done around the series. The chocolates the Himeko and Bossun were eating in the chapter were Dante was looking for his mechanical pencil, are a parody of the famous cosmic cat, and Chuu-san is referred as "he thinks like he is Doraemon or something".
Speaking of Gaou... he could be a direct shout-out to one of Hirohiko Araki's first works (Baou, from 1984-85) or well, Raoh from Fist of the North Star to reforce the old-school battle shonen genre reference in his speech.
One of the alternate universes played in the manga is a whole play on the Dragon Quest RPG format, just that it comes wrong in so... so many levels.
The song that Switch's is 'hummin' is the Overture fo the franchise too.
Bossun about comparing Koma's family sizes. Her grandpa when serving food to Cherry looked like Gandalf was sharing food with Frodo, and her dad, when standing up from the table where they were eating looked like an EVA.
Bossun comparing Koma's strength in a previous chapter as like she has the force of a titan.
Himeko's maid outfit in the Culture Festival of 2009 made her look as Hilda from Beelzebub, as pointed by Bossun.
Switch and Bossun then made a cameo in that series as well.
Saaya's fanclub is called the AGT38, a shout out to AKB 48 whose one of their units, French Kiss, sung the first opening of the anime series.
At one episode of the series, Switch can be seen playing a game about Saki
Also at one of the episodes, you can see a poster of the Vice Captain of Kazekoshi Girls School Kana Ikeda on a bulletin board.
Dante was from the very beginning a shout out to Visual Kei singers, more specifically, Gackt. Who ended up voicing him in the anime series.
In New Year's (2010), Bossun and Tsubaki are playing a game which looks similarly to Monster Hunter.
The Party! Hallelujah! single cover is based on the one of Blood, Sugar, Sex, Magik of Red Hot Chili Peppers.
A series named Mobile Force is definitely a play on some of the Gundam series as well.
Roman's peers from the other (shonen) manga club, Sainon and Magarfunkle are a reference to Simon and Garfunkle.
Funny Bunny, the song that gets sung by The Sketchbook in the anime and manga is definitely a shoutout in consideration of The Pillows. The band sung later the first ending of the series (Comic Sonic), too. Visually speaking, in the anime series, the CD that Bossun receives to practice the bass, is the Rock Stock & Too Smoking hits album from 2009.