McDonalds

McDonalds is a famous restaraunt that is secretly a crime orginization (in Mario games, at least). In some (made-up) Mario-related things, McDonalds is just a shop. It played a major role in Mario's McDonalds Madness and Nintendo Power: The Movie.

Mario's McDonalds Madness
In Mario's McDonalds Madness, Bowser, tired of paying money for Big Macs, takes over McDonalds and uses it to lift Peach's Mushroom Grill into space. Mario stops him and all is well.

Paper Mario: The Lost Laughs
In Paper Mario: The Lost Laughs, McDonalds is a shop in Luigi Landing.

Nintendo Power: The Movie
McDonalds plays an important role in NP: The Movie as the antagonist. Scrooge McDuck has somehow taken control of McDonalds, and gave it to his nephew Donald Duck and his nephew's BFF, Mickey Mouse. It is also revealed much later in the film that McDonalds was the cause of the whole storyline where the NP Staff saves the world. Despite McDonald's limited screen time, it has gone down as the best Nintendo Villain organazation ever.