When Hisao meets Shizune's father Jigoro and wonders if he avoids to see him, then he also cannot see Hisao, just like the Bugblatter Beast of Traal.
The nurse warns Hisao not to hurt Emi if he does not want to be late, as in the late Hisao Nakai, then admits that it sounded better in his head.
Shizune also makes the classic Gendo pose whilst playing chess with Hanako.
Hisao points out how needlessly repetitious this is.
If Hisao joins the student council, Misha will clap and repeat the word "Congratulations!".
At one point, Hanako also reads "Dance Dance Dance" by Haruki Murakami. If Hisao does not scare Hanako away in the library, she'll even namedrop it.
Hanako is reading a book about "a boy and a tiger on a boat".
It is also possible Kenji was referring to Jet Li's "The One", which has a similar premise.
When Hisao wonders if he is Only Sane Man, Kenji says that he is the only sane man in the school, and as a certain foreign film puts it, " there can only be one!".
After a conversation with Kenji, Hisao mentions a book he is reading a book about "an underground postal system that may or may not exist", a reference to The Crying of Lot 49.
Tea house Shanghai was originally supposed to be a Higurashi: When They Cry reference, but the devs quickly backtracked and made it a Touhou Project one instead.
Also, the chubby guy in the top right corner looks a bit like Peter Griffin.