South Park episode The Jeffersons
April 21, 2004
The sixth episode of season 8 (Episode #117), is about a person called Michael Jefferson, actually being Michael Jackson in disguise, moving to town. Near the beginning, the four main characters visit the Jeffersons' house and among the many things in it is an arcade cabinet with the title Thurst for Blood on it, but the game footage is actually from Super Mario Bros. 2.
South Park episode Imaginationland
October 17, 2007
The tenth episode of season eleven of South Park, titled "Imaginationland" (also known as "Kyle Sucks Cartman's Balls") is about Stan, Kyle, Kenny, Butters and Jimmy visiting Imaginationland, a land where all imaginary characters live together. Among them is a character looking almost identical to Mario, precisely in his Small Mario form. The most notable difference is the letter on his hat instead of being an uppercase 'M' is a lowercase 'm' rotated by 90°, therefore looking like an 'E'.
South Park episode Imaginationland, Episode II
October 24, 2007
The second part of the Imaginationland trilogy is about the terrorists braking the barrier dividing the good side of the imagination from the evil side, so all imaginary evil characters start attacking the good ones. Among them is a character looking almost identical to Wario, the most notable difference being the letter on his hat and gloves, that's a 'V' instead of a 'W'.
South Park episode Imaginationland, Episode III
October 31, 2007
The third part of the Imaginationland trilogy features the final war between good and evil characters. The Mario and Wario characters from the previous episodes are seen again, and this time there also is a Bowser look-alike.
At the beginning of the episode Wario is seen marching with all the evil characters, holding a shotgun, while Mario is seen shortly after, taking a sword that's almost three times his height and preparing for battle. Later, as the battle begins, Wario is seen holding a spear, while a short Bowser look-alike can be seen. Mario is later seen charging with his sword and again at the end of the episode celebrating with all the other good characters.
South Park episode Royal Pudding
May 11, 2011
The third episode of season fifteen of South Park, titled "Royal Pudding" is about the Princess of canada being abducted during her wedding, so all canadians are called upon to help save her, and Ike is among them.
While being abducted the princess is trapped in a cubic force field, possibly referencing how Princess Peach is trapped in a cube during Super Paper Mario. The reference to Mario is made stronger by the appearance abong the canadians of "The Little Mushroom People of Nova Scotia", most likely parodies of Toads from the Mario series. Finally, the monster who kidnapped the princess, Tooth Decay, is a large green creature with spikes on his body, possibly based upon Bowser.
The Fractured But Whole
October 17, 2017
One of the memberberries in The Fractured But Whole mentions a reference to collecting 120 Stars in Super Mario 64.
South Park's company Comedy Central had no right over Nintendo's characters, so they could only do subtle references.