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Possibly the scene of Oddish wiping away Misty's tears in the episode 10 "Bulbasaur and the Hidden Village" was an influence for Ken Sugimori in creating the western version of Misty's Tears card.
Misty's Togepi was one of the few who saw the Three Legendary Beasts of Johto: Suicune (EP114 Don't Touch That 'dile), Raikou (EP180 Houndoom's Special Delivery) and Entei (Movie Spell of the Unown).
In episode 160, Air Time!, Misty wears an outfit which pays homage to the heroines of manga, anime and videogames from the decade of the 80s.
The earrings and pearl necklace on Sygna Misty's head are a clear influence from her appearance as a mermaid in the anime.
Misty had a Gyarados in the Dengeki Pikachu and Pokémon Adventures manga before having her own in the anime series.