These are the only ones I found.
> 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 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.