The Mario series has the most common Easter Eggs across Nintendo’s series. They have appeared in Zelda, Donkey Kong, Yoshi, Animal Crossing, and even Banjo-Kazooie games.
In Donkey Kong Country 2, Mario appears as the first Greatest Video Games Hero who collected the most DK Coins after Diddy Kong and Dixie Kong defeat Kaptain K. Rool. To catch up with Mario and take his first position, you need to help Diddy Kong and Dixie Kong collect all DK coins in every world, including the secret Lost World deep within Crocodile Isle.
Mario also appears in Donkey Kong 64, but only when Donkey Kong accesses the Donkey Kong arcade, where you must play as Mario to rescue Pauline in the first level and then the N64 coin in the second level.
In Zelda games, Mario appears as a painting in A Link to the Past to release Rupees if Link pulls on the painting. Chain Chomps also appeared as Easter Egg enemies.
In Ocarina of Time, Mario, Luigi, Peach, Yoshi, Toad, and Bowser appear in pictures found inside the room sealed with windows to the right of where you meet Zelda. If you shoot a Deku Seed at it with a Slingshot, it releases a Red Rupee. In the 3DS remake, they are replaced with a World 1 background in New Super Mario Bros.
In Majora’s Mask, you can see the Happy Mask Salesman carrying Mario’s Mask on his bag while on a quest to stop the Moon from falling down to Termina.
In Link’s Awakening, you can encounter Goombas, Piranha Plants, Pokeys, Cheep Cheeps, Shy Guys, Boos, Spinies, Poodaboos, Chain Chomp characters, and Bloopers as Easter Egg enemies. Yoshi appeared in Link’s Awakening, but as a doll that can be given to a specific character to begin the Trading Quest. You can also see a picture of Princess Peach mentioned in a letter that must be taken to a specific recipient during the Trading Quest. You can even meet Wart, who also appeared in Super Mario Bros. 2.
In Oracle of Seasons, you can encounter Poodaboos, Cheep Cheeps, and Pokeys.
In The Minish Cap, Lakitus, Spinies, and Bob-ombs appear as Easter Eggs enemies. Also, if you head a caterpillar enemy with the sword, it gets mad just like a Wiggler.
In the original Hyrule Warriors, you can unlock the strongest tier of Link Gauntlets that have a Chain Chomp as an Easter Egg.
In Tri-Force Heroes, there is an item that shoots fireballs with an Easter Egg fireball sound from Super Mario Bros. There is also an unlockable outfit that will make you look just like a Hammer Bro from the Super Mario Series.
There are enemies and collectibles that you can also encounter in Metroid games.
In every Animal Crossing game, you can get clothing and furniture that belong to the Mario Series, including the Mario Theme, Big Bros’ Hat, and Li’l Bro’s Hat. However, in the Mario Theme, there is a criterion in each Animal Crossing game to obtain all the furniture from the Mario Series.
In Banjo-Kazooie on N64, you can find a mustache face that looks like Mario’s if you enter a specific location with the Jigsaw Piece in Gobi’s Valley while venturing in Gruntilda’s Lair to rescue Banjo’s sister, Tooty.
In Kirby Super Star, there is a minigame called Megaton Punch where Birdo, Mario, Luigi, and Toad appear as Easter Eggs in the crowd while Kirby beats all three competitors by earning a higher score than them.
In the NES game Punch-Out!, Mario appears as a referee. In the arcade games Punch-Out! and Super Punch-Out!, Mario and Luigi appear as Easter eggs in the crowd on both sides when you manage to help the Challenger knock down every enemy boxer. In the SNES game Super Punch-Out!, names including Mario, Luigi, and Peach appear in the time record lists until most players with a registered name beat their records after beating certain boxing opponents. In the Wii Version of Punch-Out!, Doc Louis mentions the plumber, possibly Mario, when talking to Little Mac during corner break intermissions with Donkey Kong.
In one of the two versions of Mega Man Battle Network 3, Yai’s house has a red cap and blue overalls hanging on the northeast wall. Those Easter egg clothing pieces must have presumably belonged to Mario.