Natsu no Arashi! (TV)

Episode 1 around 15.00 is a reference of Sayonara Zetsubo Sensei.

in ep 2 at about 15:46 you can see tenma and harima from school rumble in the cafe. a reference to the authors other manga & anime school rumble

in ep. 8 at about 4:07 you can see a 86 in the background. a reference to the manga and anime series Initial D and also a nod to when the author made use of the car when hanai was hit in the school rumble anime

Episode 12 around 9:03. The crest of the weather vane is replaced by a reference to NAB's (The National Association of Commercial Broadcasters in Japan) mascot named Chidejika ("Chidejika" for "terrestrial digital broadcasting transition," and "shika" for deer).

Episode 13 around 4:10. The crest of the weather vane is replaced by a bust of Marisa (from the Touhou game series), and is portrayed in the "take it easy" or "yukkuri" form.

Episode 9, the book Yayoi is talking about in the opening and ending is Sayonara Zetsubō Sensei.

Episode 13 11:40 Sayaka is dressed like Sakura from Hyper Police.

In the closing of episode 2, Yayoi is, of course, talking about Doraemon, and playing up the parallel between Hajime and Nobita.

At the beginning of episode 9, the four protagonists of Hidamari Sketch are seated at the table next to the coffee house bar.

The insert song "Southpaw" was originally made famous by Pink Lady in 1978.

The insert song "Dōnimo Tomaranai" was originally made famous by Linda Yamamoto in 1972.

The insert song "Koi no Dial 6700" was originally made famous by Finger 5 in 1973.

In episode 5 around 7:20 the two people asking for Jun's number while serving them look like Amuro Ray from Mobile Suit Gundam and Char Aznable in his Quattro Begeena alter ego from Mobile Suit Zeta Gundam, but with their hair color swap.

In episode 9 - 4:01 up to 4:04 - While the master is asking Kaya and Arashi to Time jump taking with them the rotten Mackerel Sashimi (to be able of been eaten - urgh) The Dorm Leader and Father Toichiro Kanae - both from Maria Holic are sitting in a nearby table

In episode 12, around 9:19, you can see G Gundam's Domon Kashu and Master Asia in the cafe talking to Yayoi

In episode 13 at 5:38 the milk carton has a picture of Tenma from School Rumble drinking milk while at 11:40 it shows Eri on the organic milk carton. Another School Rumble refernece in this episode is that they are all wearing a unifrom in the cafe similar to that of the School Rumble uniform complete with Tenmas pigtails. Jun is the one who is wearing something that looks the closest to what the actual unifrom is like.