When Mario and Toad try to enter Princess Peach's castle, two toad guards joke that "the princess is in another castle". This is a reference to the original Super Mario Bros. (1985), where at the end of each world (bar world 8) a toad said "Thank you Mario, but our princess is in another castle".
A game cabinet in the pizzeria early in the film is called "Jump Man." The character of Mario was originally known as "Jumpman" when he first appeared in the video-game Donkey Kong (1981). The character's name was changed to Mario as a tribute to the landlord of Nintendo of America's warehouses, Mario Segale.
When Luigi's phone rings, his ringtone is the startup jingle from the Nintendo GameCube. The default caller icon also resembles the default Mii on the Nintendo systems since the Wii.
One of the residents in the Mushroom Kingdom is seen buying a Nintendo Entertainment System (NES) cartridge at the antique store. The owner of the store tells him to blow into it to get it to work, a reference to what you had to do to get the game playing
The music played during Mario and Luigi's plumbing commercial is actually the theme music of the kid show The Super Mario Bros. Super Show! (1989), starring Lou Albano as Mario and Danny Wells as Luigi.