Creatures, Inc.
Chee-Chai Alien
Saraba remarks at the beginning of the game while explaining the game that "(it's) like Pokémon, isn't it?". One of the minigames, known as "Mystery Circle" (Japanese: ミステリー サークル) features "!" marks similar to the ones in Pokémon Red, Blue, and Yellow, Pokémon Gold, Silver and Crystal. It is the signature memory of Tenrē (No. 045).Game Freak
Drill Dozer
The School Girl Clothes are the same clothes as Leaf from Pokémon FireRed and LeafGreen. Other clothes reference characters from different franchises, such as Mario, Pulseman and Click+Medic; the latter belonging to Game Freak. Detailed on this page.HarmoKnight
The basis of this game may have been influenced by a minigame in a Nintendo Space World 1997 demo of Pokémon Gold and Silver (later leaked in four revisions), in which Pikachu must collect musical notes. Features Pokémon themed stages and music, see Bulbapedia article.Pocket Card Jockey
Names of horses reference Pokémon and other Game Freak games:1. Pikapika Mouse (Pikachu)
2. Bullet Seed (grass-type Pokémon move)
3. Gold Heart and Silver Soul (referencing Pokémon HeartGold and SoulSilver Versions)
4. Bulba Soarer (reference to Bulbasaur)
5. Smart Ball (referencing the US name of a 1991-1992 SNES game by Game Freak)
6. Mocket Ponster (referencing Pokémon)
The text "Gotta get 'em all!" appears.
(Source for above cameos)
Pulseman
Various; in particular Pulseman's home computer Saint Ann inspired the name for the S.S. Anne. There are also music similarities to tunes in Pokémon Diamond, Pearl and Platinum. See Bulbapedia article.Nintendo
Many covered on Bulbapedia, see: List of references to Pokémon in popular culture, List of Pokémon parodies, List of background references to Pokémon.Some of the non-Pokémon games in which Pokémon have appeared or have been mentioned include:
Game Boy Camera: Pokémon stamps StreetPass Mii Plaza: Pokémon X and Y puzzle panel, appearance of Junichi Masuda as a special Mii Nintendo Badge Arcade: Mentioned by the Arcade Bunny, and many Pokémon badges were released Picross NP: Volume 1 covers Pokémon puzzles Splatoon splat-fest ('Pokémon Red VS Pokémon Blue') Super Mario Maker: Pokémon Mystery Mushroom costumes from their Super Smash Bros. amiibo.; a Pokémon Event Course called "I Choose You!" celebrating the 20th anniversary of Pokémon Super Smash Bros. series: Many elements of Pokémon have appeared in the games, ever since the original for Nintendo 64. As of Super Smash Bros. Ultimate, Pikachu, Pichu, Jigglypuff, Mewtwo and Greninja are playable characters. Trade & Battle: Card Hero: "Rocket Monsters" reference by an NPC
This list is not intended to be exhaustive.
References to past Game Freak games within Pokémon games
Bushi Seiryūden: Futari no Yūsha
(speculative): The unused song exclusive to Pokémon Yellow sounds like one of the boss encounter themes from this game. (speculative): Wokuu and the Pokémon Victini have some design similarities.Mario & Wario
In the Mimic Girl's room, there is a SNES console which displays the text "A game with MARIO wearing a bucket on his head!" when examined, which is a reference to this game. Part of the sky theme music sounds very similar to the later Pokémon Red, Blue, and Yellow Route 24 theme.(Source)