- All of chapter 2 of Thousand-Year Door, in which you command an army of tiny critters with a long, singular antennae on top of their heads, is a pretty clear reference to Pikmin.
- The Pikmin references don't stop there. The space helmet that you wear in Chapter 4 of Super Paper Mario bears an uncanny resemblance to Olimar's helmet.
- There are MANY references to Mario & Luigi.
- In Thousand-Year Door, Bobbery will request you bring him Chuckola Cola.
- Also in Thousand-Year Door. Bowser will attempt to steal a fake Crystal Star. When Pennington questions him, you can make Bowser call himself The Shadow Thief. On top of that, he will say "I'll be taking this, thanks!"
- In Super Paper Mario, Mr. L will call himself The Green Thunder, a reference to Luigi's thunder ability in Mario & Luigi: Superstar Saga.
- Another one for TYD, Mario will eventually get an email from the real Zip Toad, who ends his message with an inspiring line from one of his movies. The movie's name? The Toad Warrior, named after a The Super Mario Bros. Super Show! episode, which itself was a Shout-Out to Mad Max 2: The Road Warrior.
- The Great Sea area in Paper Mario: The Origami King is one long Shout-Out to The Legend of Zelda: The Wind Waker, down to the name.
http://tvtropes.org/pmwiki/pmwiki.php/ShoutOut/PaperMario
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