In one What If? omake Tomoko is shown reading Tonari no Kaibutsu kun. 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.
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).
When Tomoko goes to the book store, the manga she picks out is Kitakubu Katsudou Kiroku, which also happens to be published by Square Enix and got an anime adaptation in the same season as Wata Mote.
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.