* The place where Maddison Hayes' final "boss battle" was fought was called Coeur Tower. As in [[VideoGame/DigimonWorld2 Core Tower.]]
** The three original leaders of Team Liberty also got their codenames from the Guard Teams in Digimon World 2--Gold Hawks, Blue Falcons, and Black Swords (with "Swords" being replaced with "Skull" in Blackskull's case.)
* Both Sleight and Meghan Vert have ordered their Pokémon using the phrase, [[VideoGame/BioShock1 "Would you kindly x?"]].
* Koga's execution of Nemo Buck was deliberately modeled after the plot-relevant assassinations in Franchise/AssassinsCreed.
* During a training battle between Ray and Sonja, Ray's Dewott used a spinning Aqua Jet attack written in such a way as to invoke the 3D Maneuver Gear from Manga/AttackOnTitan.
* [[ThePhoenix Ho-Oh's]] [[TheNthDoctor regeneration ability]] was based off of those of [[Series/DoctorWho The Doctor]].
** On a similar note, a mysterious and slightly grumpy [[Series/DoctorWho Doctor]] and [[Characters/DoctorWhoRevivalSeriesCompanions his companion Clara]] treated both Alex Zyther and Amelia Zann's Carvanha "Van"; during the "Summer Wars" arc in Celadon City, the pair vanished into thin air, though Zann's Larvitar Harvey heard a "[[Main/SignatureSoundEffect strange (mechanical) whine like nothing in the world he had ever heard of]]" shortly after said disappearance.
* Sheik's nickname came from Franchise/TheLegendOfZelda.
** Similarly, with [[Film/{{Inception}} Ariadne's]].
* The description, "Dark-haired, fire-based baritone [[BadassInANiceSuit In A Nice Suit]], FatherToHisMen military man" could easily apply to either Shadow Admin Sleight or [[Manga/FullmetalAlchemist Roy Mustang]], although WordOfGod says that this was unintentional.
* Lafoyae Belrose and Jackson Sang are direct shout outs to Literature/{{Baccano}}, which also inspired the initial stages of the [[TrainJob story arc]] that they were introduced in.
* [[TheNicknamer Gold]] consistently referred to Ray as [[Manga/{{Bleach}} Ichigo]] during the Unova Arc, due to the characters' similar appearances.
* While investigating the situation in the Celadon Department Store, Ethan orders the group to [[Franchise/ScoobyDoo "Split up. Look for clues."]]
* [[UnstoppableRage Wrath's]] last words were a direct shout-out to Lust's from Manga/FullmetalAlchemist.
* Three of Team Zephyr's members have been crafted as expies or blatant references, purely for the sake of [[RuleOfFunny comedy]].
** Skyler's mannerisms and appearance are a straight-up expy of [[{{Franchise/ScoobyDoo}} Shaggy Rogers]], complete with a team consisting of a Houndoom named Scooby-Doom, an Ursaring named Teddy Jones, a Klingklang named Velma Klinkly, and a Swanna named Daphne [[WesternAnimation/LooneyTunes Duck.]]
** Skylark is obsessed with music, has a brother named Chip, and is part of a band with said brother called the [[{{WesternAnimation/TheFairlyOddParents}} Chipped Skylarks]].
** Skye's Pokémon are all named after superheroes. So far she's obtained The Human Torchic, Spinarak-Man, and Zubatman.
* Soil Colossus, Inc.'s entire organization was one big shout out to [[{{Website/Smogon}} Smogon's]] CAP project Collossoil.
* The introduction of the Pokémon Rangers to Sootopolis, showing them descending toward the city from helicopters on the backs of their Flying-Type Pokémon, was a direct reference to the Volume 2 opening from {{WebAnimation/RWBY}}
** Quentin Dallas's appearance is also directly based off of Roman Torchwick's. Their mannerisms aren't far off from one another, either.
* James and Guinevere apparently once lived in the same orphanage as the [[{{Film/TheBluesBrothers}} Blues Brothers]], if Celadon is actually Chicago.
* Alma Mason is a general shoutout to survival horror games' love of creepy children, but she was named after two characters from such franchises. Her first name is a shoutout to the character in [[VideoGame/FirstEncounterAssaultRecon FEAR]], while she shares her last name with the protagonists of the [[Franchise/SilentHill Silent Hill]] games.