In chapter 50 Kotomi is shown reading the 17th volume of Kino's Journey.
In chapter 56 Tomoko watches My Little Pony: Friendship Is Magic. This is also a shout-out to Kitta Izumi who played Tomoko in the anime and also dubs the voice of Rainbow Dash in Japan. Later in that chapter, while playing basketball during her P.E. class Tomoko tries (and fails) to pull off Ignite Pass Kai.
In chapter 72 Tomoko, realizing that she'll have to interact with Yoshida, Yuri and Ucchi on the first night of the school trip, quotesVegeta.
In chapter 89 the books picked by Kotomi for the recommended section of the school library are again stand-ins foractualbooks. Later in that chapter Kotomi blissing out while lying in Tomoki's bed looks a lot like Baki Hanma triggering endorphins in Baki the Grappler.
In one What If? omake Tomoko is shown reading My Little Monster. She then breaks the fourth wall to comment that her life would be much more fun if the author of that manga were also the author of her story.
In an omake set immediately after chapter 107 Tomoko asks Hina Nemoto what her favourite anime is (to mock her taste in the anime). Hina starts giving an honest answer (she doesn't finish the sentence, but it seems to be Girlish Number), but flip-flops when Okada walks up to them and claims to like Your Name.
In chapter 109 Tomoko recommends a book from the Kino's Journey series to Yuri and mentions the movie Tomorrow I Will Date With Yesterday's You. Also, when Yoshida asks her to pick a book for her, Tomoko looks for works of Ai Yazawa.
When Tomoko stumbles upon a porn DVD about a high school older sister in black tights, she immediately gives a pair to Tomoki as his Christmas gift. This is a reference to a Tomoki/Tomoko WataMote H doujin made around that time, which heavily made use of Tomoko in pantyhose.'
One T-shirt of hers has "Spark" written in the Star Wars font.
The scene where Tomoko searches the Internet for the information on how to make herself prettier parodies Light Yagami's killing spree from the first episode of the Death Note anime (and she begins her search at Gaagle).
Among the terrible fates Tomoko wishes on her classmates are being attacked by the midget aliens from Gantz and Shimada from Parasyte.
One of the games Tomoko plays at the beginning of the episode appears to be Kiniro No Corda, looking at that Yunoki CG.
In episode 3, many of Tomoko's fantasies take place in the world of Animal Crossing.
When delving into one of her erotic fantasies in episode two, Tomoko finds herself curled and severely wounded inside a crater much like Yamcha's death in one of the early episodes of Dragon Ball Z. The pose is back for episode 5.
In episode 6, the cover of the game she's playing at the beginning (Planetary Prince Gachi Love 8108%) resembles Uta No Prince Sama (whose anime adaptation is called Uta no Prince-sama Maji Love 1000%).
Episode 10: Tomoko mentions how before joining school she dreamt of meeting Kazehaya-kun. In her delusion about the Everyday Club, the girl looks like a brown-haired Rikka, and the club distribution looks very similar to the one of the SOS Brigade.
In episode 12, after Tomoko secretly records her classmates, she finds out they're not talking about her at all. She then wonders if her classmates deliberately ignore her, and imagines herself as Mei Misaki from Another. Coincidentally, it doubles as an Actor Allusion in the dub.
The cockroach sequence references Terra Formars, where humans battle mutated roaches.
Meanwhile, the "God Knows" sound-alike from episode 11 is playing.
During Tomoko's Imagine Spot where she pictures herself visiting a Purikura with two friends, the three of them perform the military salute from Attack on Titan.
Immediately after, the scene wherein Tomoko's high school life note indeed the events of the previous 11 episodesflashes before her eyes accompanied by a distorted overlay and disconcerting train sounds is an homage to a similar scene from The End of Evangelion.