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Despite Shuten dōji, the yōkai Thurston is directly based off of, being known for being a heavy drinker, Thurston's Yo-kai Medallium Bio in Yo-kai Watch 3 states that the contents of his rice wine cup is a sports drink, due to him losing too many fights while intoxicated.
Harry Barry is based off of the mascot of Kumamoto Prefecture in Japan, Kumamon.
Samugarriku Chopin is based off of the Polish composer, Frédéric Chopin. However, Samugarriku Chopin's name is a combination of Frédéric Chopin and Pupsicle's Japanese name, Samugari, despite Samugarriku Chopin being a variant of Chilhuahua (whose Japanese name is Gariouji).
Arachnus and Toadal Dude can be seen fighting in the background of Episode 7 of the anime, "Mr. Osomatsu 2nd Season."
The Quest, "The Provincial Publicity Project", from Yo-kai Watch 3, involves Directator filming a movie that stars Komasan and Komajiro. The movie is titled "Koma's Name", and its name and teaser trailer parody the popular light novel and movie, "Your Name." (2016)
Upon defeating Shishiguro in Yo-kai Watch Jam - Yo-kai Academy Y the Movie: Can a Cat be a Hero?, Kengo Benimaru says: "I sliced someone unworthy once again". This is a reference to an iconic quote from "Goemon Ishikawa XIII", in the manga and anime series, "Lupin the 3rd".
Furgus is based off of the real youkai from Japanese folklore, Keukegen (which is also Furgus' Japanese name), a hairy, dog-like youkai, said to have been responsible for making people sick.
When Robonyan F's car gets hit by B3-NK1 in episode 119 of the Yo-kai Watch anime, he turns into several spinning heads that resemble the Osomatsu brothers from the manga and anime series, "Osomatsu-san".
Episode 43 of the Yo-kai Watch anime features the character "Professor Vacant" in a TV show Nate is watching, who is a parody of "Professor Hershel Layton", of the "Professor Layton" series. Professor Vacant's theme music, (which can be heard in this episode,) is a remix of (1/2)
Professor Hershel Layton (Professor Layton), Asuto Inamori (Inazuma Eleven), Jibanyan, Chup (Snack World), and Evan Pettiwhisker Tildrum (Ni no Kuni)'s silhouettes make appearances in Shadowside Hinozall's Soultimate Move in Yo-kai Watch Puni Puni, referencing LEVEL-5 IPs.