February 27, 1996
In Saffron City there's a character named Copycat. Walking in her room and checking the TV will make the player character say that there's a game with Mario wearing a bucket on his head. That game is clearly Mario & Wario.
This reference was kept in Pokémon Yellow.
Pokémon Stadium Gold Silver
December 14, 2000
Pokémon Stadium Gold Silver, known outside Japan as Pokémon Stadium 2, features a Game Boy compatibility that allows to bring "Mistery Gift" items from Pokémon Gold, Silver and Crystal in to the game. These are decorations for the player's character room and include NES, SNES, Virtual Boy and Nintendo 64 consoles. When connecting one of these consoles (except for the Virtual Boy), the TV will show an image from a Nintendo game for that console. Mario games that may appear are Super Mario Bros., Super Mario World and Super Mario 64.
Super Mario Galaxy
November 01, 2007
A little planet in the Buoy Base Galaxy in Super Mario Galaxy seem to be shaped like a Poké Ball.
Super Mario Galaxy 2
May 23, 2010
The Fluzzard bird in Super Mario Galaxy 2 looks very similar to the Ho-Oh pokémon.
Super Mario Maker
September 10, 2015
Six of the unlockable costumes that Mario can wear in the game by using a Mystery Mushroom are based on Pokémon, specifically: Pikachu, Charizard, Jigglypuff, Mewtwo, Lucario, Greninja. All of them are based specifically on their overworld sprite from the Nintendo DS Pokémon games, exept for Greninja who debuted in the Nintendo 3DS games Pokémon X and Y, and therefore has an original 8bit design. Unlike most other costumes, these costumes don't affect the sound effects when worn. They can be unlocked in the 100 Mario Challenge mode or alternatively by using the respective amiibo from the Super Smash Bros. series.
An update later also added costumes based on Bulbasaur, Charmender and Squirtle.
Copyrights for both series are held by Nintendo.