In the core series
In the Generation I games and Pokémon FireRed and LeafGreen, in the Copycat's room there is a television connected to a Super Nintendo Entertainment System running "A game with Mario wearing a bucket on his head!", referring to the Japan-exclusive game Mario & Wario, also developed by Game Freak.
In the Generation I games and Pokémon FireRed and LeafGreen, PokéManiac Ashton in the Rock Tunnel makes a reference to Mobile Fighter G Gundam, saying "Pokémon Fight! Ready, Go!" prior to battle. Official Gundam Fights in the series began with both participants declaring "Gundam Fight! Ready, Go!"
In Pokémon Platinum at Victory Road, Ace Trainer Omar says, "One day, people will run to the other side of the road when I walk by 'em." This may be a reference to Omar Little from the series The Wire where people often run away when they see him walking down the street.
In the English versions of Pokémon Black and White, two Driftveil Gym Pokémon Trainers (Clerk Isaac and Worker Felix) who use Ground-type Pokémon share their names with main characters from the first two games of the Golden Sun series, who are both associated with the element of earth.
In Pokémon X and Y, after being defeated by the player, Preschooler Mia on Route 4 says "Hey! Hey! Listen!" before battle, referencing Navi from The Legend of Zelda series.
In Pokémon X and Y, Veteran Timeo in Victory Road will say "my body is ready" before battling the player, a reference to the meme spawned from a statement made by Nintendo of America's President and COO Reggie Fils-Aime at the unveiling of the Wii Balance Board at E3 2007, "My body… my body is ready!"
In Pokémon X and Y, the final chapter of The Looker Detective Agency is named "Here's lookin' at you, kid", a reference to Humphrey Bogart's quote in Casablanca.
In Pokémon Omega Ruby and Alpha Sapphire when the language is set to French, before battle Brawly says, "J'ai découvert le secret de la vraie puissance en fixant un Nautile pendant des jours et des jours…", a reference to Twitch Plays Pokémon.
In Pokémon Sun and Moon, if the player takes a picture of water while using the Poké Finder, one of the possible comments is "7.8/10 Too much water ¯_('-- ')_/¯", a reference to the meme spawned by IGN's infamous review of Pokémon Omega Ruby and Alpha Sapphire.
In the side series
In Pokémon Stadium 2, when the player views the entire room, if a game system other than the Virtual Boy is set up, screenshots from several games for that system (such as The Legend of Zelda: Ocarina of Time for the N64) will appear on the player's TV.