In Yu-Gi-Oh! GSTART, Kohaku Yudin's Pixel HERO Deck includes multiple Monster Cards that reference this series (among others), including Red Hammer (Mario), Green Jumper (Luigi), Crown Parasol (Peach), Muscle Kong (Donkey Kong), Red Blazer (Fire Mario), and Red Freezer (Ice Mario). According to the author, Kohaku's design also includes a few cues from Mario, such as his red shirt, white gloves (shared reference to Sonic), and red M-shaped fringe in his hair.
Film - Animated
Wreck-It Ralph has a few references to the series, despite not having the brothers themselves.
Dino Attack RPG: Doctor Marco Martinet started a reference to the Dr. Mario games before expanding to being inspired by the Super Mario Bros. series as a whole. His brother, Louie Martinet, is based upon Luigi, his cousins Warner and Wallace are inspired by Wario and Waluigi, and his former love interests Pearl and Primrose are inspired by Princess Peach and Pauline, respectively. Additionally, the sports Martinet participated in his youth (including going to the Olympics) are references to various Mario spin-off games.
Rosalie Mercedes is based upon Princess Rosalina from Super Mario Galaxy. Her first appearance flying into the final battle with a fleet of T-1 Typhoons following her and destroying Fright Knight windships was inspired by the cutscene in Super Mario Galaxy'' featuring Rosalina flying into Bowser's Galaxy Reactor and destroying the airships that guarded it.
One comment thought the Maelstrom had been created by a chaos heart and needed pure hearts to defeat it, referencing the Void created by Count Bleck in Super Paper Mario.
Astérix and Obelix XXL2 have several references to the series:
Even before entering Las Vegum proper, you'll face the first special Roman soldier. He has a big moustache, a helmet with a red Roman Eagle shaped like a M, and turtle shells as shoulder pads. He's equipped with a FLUDD device (Super Mario Sunshine was the most recent entry of the main series at the time of XXL 2's development). When defeated, these Mario Soldiers emit a muffled "Mamma mia!" They get some statues on the Arc de Triomphe, and small flags near the Eiffel Tower.
A transition room in Venetia has the faces of Mario and Luigi◊ near the two big buttons. The buttons themselves are of the same red and green as the Mario brothers.
Later in Venetia, in the square inside the giant dark hall, you can see several statues, among them Princess Peach and a Shine Sprite (you can find two more a little later).
In the large courtyard at the beginning of WCW, there's a big green pipe◊. You can enter it and find an entire Mario-themed area. There are floor mosaics of carnivorous plants, tiles of mushrooms, flowers, banana peels and Shyguys, unstable platforms shaped like Shine Sprites and POW blocks, and Thwomp-like devices◊ (although they are designed to make you fall rather than crush you).
Also in the exterior areas of WCW, there are two◊ small◊ Mario-esque artificial hills that stand out evidently.
At the end of WCW, before entering Pirate Island, you can notice wall tiles reproducing Super Mario blocks.
An area in Kingdom of Loathing has you fighting Goombas, Koopas, Buzzy Beetles, Bullet Bills, and Bloopers. The Buzzy Beetles only appear after you ascend once, a reference to their appearances in the New Game+ of Super Mario Bros..
Also, one part of the fight against a Goomba has this message:
In Lollipop Chainsaw, Juliet's super-mode has her change a variety of different colors, and a special music plays ala Mario once he gets a star.
During the Fulci Fun Center stage:
Nick: Alright, this is all too surreal. If a little dude in a red cap and blue overalls pops out at me I am seriously gonna vomit all over myself.
The emblem reward for getting ten kills in a row while having no killstreaks equipped in Modern Warfare (hence worth trying only for this) is an 8-bit image of Capt. Price that looks exactly like Mario's Super Mario Bros.. 1 sprite.
Mariofield edits a Christmas-themed strip. In the original, Garfield gives Jon the "Box O' Mystery", which turns out to be empty. In this version, the box is a Question Box and it contains a Poison Mushroom.