- Eggman saying "Welcome to your doom" to N in "The Ideal Hero".
- From the same story arc, Eggman's attempt at a Dr. Weird impression which the heroes and heroines find unfunny, which is also a reference to Robotnik Shorts.
- Also from "The Ideal Hero" story arc, "No freaking way!" being Sonic's reaction to Black Kyurem.
- Near the end of part 4 of "The Ideal Hero", Sonic sings a modified version of a part of the lyrics to City Escape.
- The fact that the Side Story spinoff fics have story arcs that are composed of four parts each and in addition, focus on characters who either don't appear in the main stories at all or who don't appear all that often resembles the Sonic Universe comics, which had four part story arcs and focused on characters who weren't as prominent in the regular Sonic comics.
- In the main story "Group Discussion", while the PDP members are thinking of ideas for plays Hilda and Shizuku could perform for the Theatre Club, the video games Pokémon X and Y and Fray in Magical Adventure are referenced and the Fairy Tale Peter Pan is suggested until Shiori suggests Little Red Riding Hood to which everyone agrees.
- Risa's surname is a nod to Kathy Selden, a character from the 1950s movie Singin' in the Rain.
- Honoka references Aikatsu! by name and mentions something about Stands in "Pokémon S.T.A.R.T!!".
- The title of "Otonokizaka, I Choose You!" is a reference to both the debut episode of the main Pokémon anime as well as the 20th Pokémon anime movie.
- On the FANDOM wiki for the AU, a heading used for the page on non-canon characters uses a sprite of a Big Boo from Super Mario World.
- Shizuku mentions the Ys series by name when comparing the music for a nonexistent game she reviews in "Nintendo Dream Guest Reviews!".
- Kasumi says "Let me tell you a story" as part of one of her lines in "Decision, Decision!".
- In "Funyun Schumnyun!", Shizuku tells Shigeru Miyamoto to "Zip it" while pointing at him, just like a scene in Deadpool: No Good Deed, where Deadpool does the same to Stan Lee. It helps that Live Action!Deadpool is played by Ryan Reynolds, who also has two roles in Pokémon Detective Pikachu.
- The bad future Classic Sonic discovers as well as his promise to help avert said future as well in "Prophecy of Failure!?" is an allusion to the Good Future/Bad Future mechanic of Sonic CD.
- In "A Day in the Life of a High Schooler!", Osako says "How you doin'?" in a manner not unlike Joey.
- "Singin' in the Rain!" has a few shoutouts:
- The title itself is a reference to ''Singin' in the Rain", and the Nijigasaki High Theatre Club members even quote a few lines from the movie.
- Sonic asks Hilda if Skynet is the villain in the musical.
- Near the end of the story, Sonic makes a reference to Shao Kahn's Outworld Tournament as well as the The Second World Warrior Tournament, the former of which was part of Kahn's and Shang Tsung's plan in MKII and the latter of which M. Bison was the host of in Street Fighter lore.
- Sonic says "Long time, no see!", which was a greeting certain characters have used throughout some of the 3D Sonic games.
- The "Hilda and Setsuna Yuki:Maximum Metal" arc has it's share of shoutouts:
Shout Out / Tokimeki PokÚLive! and TwinBee