In STAPelz #21 ("In the Name of Lava"), the villian King Kalatie is based on King Kaliente in Super Mario Galaxy, along with the way Captain Tonnybrow fights him. In the same issue, Promethius the Lava Robot is based on Prometheus in Meet the Robinsons the Video Game along with the way Captain Tonnybrow fights him.
The STAPelz issue #22 ("Raiders of the Lost Arcade"), there is a bunch of references to classic arcade games, such as Donkey Kong and Space Invaders.
There are dozens of references in "Follow the Rainbow Brick Road" (an undetermined number in the 30s in STAPelz). The title, for one, is a refernce to MarioKart Wii and the Rainbow Road. Also, all of the booths at the Purple Coin Fair are levels with Purple Comets. One of which is Luigi's Purple Coins.
Also, in "Rainbow Brick Road", at the Purple Coin Omlet diner, at the buffet is a dragon (Gobblegut) who is 'eating all the food'. An employee holds a fork and says "I'll take care of this." and pops all of Gobblegut's bellyache bulges.
In "The Ruler of the Galaxy's Story", the star soliders are waiting for their mother, a la Super Mario Galaxy.
There's a street in the Land of Wii that's called "Enix Square", a references to Square Enix, who made the Final Fantasy games. On Enix Square, there is a girl wearing a white robe, ordering a hot dog. Along with her hot dogs, she asks for mustard. She is a parody of White Mage, who, in Mario Hoops 3-on-3, is voiced by Denna Mustard.