The file that contains the character scripts for Kertsi is named "Navi". Since Kertsi plays a similar role to that of Navi in The Legend of Zelda: Ocarina of Time, this is likely a reference to said game.

The game contains files for Super Mario Bros. 3's Ptooie enemies, suggesting that at one point they were planned to be included in the game.

In the scrap-filled area in Shy Guy Jungle, hidden among the scraps of trashed paper are the following two messages:



Parakarry was a party member from Paper Mario, while Goombella was a party member from Paper Mario: The Thousand-Year Door. These are the only two references to earlier Paper Mario titles in the game.

Additionally, a third message can be found in the trash heap which simply reads "XD3R-B8HH-9ZR2-FL16". Despite resembling a Club Nintendo or Nintendo eShop code, it registers as invalid when you attempt to input it on either service, and no further information emerged over the years regarding its significance.

The game contains several unused stickers:
• A bigger version of the Leaf sticker.
• A Piranha Plant sticker.
• A Rock sticker.
• A Spiny Egg sticker.
• A Super Leaf sticker.

While using the Boom Box Sticker in combat, a remixed version of the Space World theme from Super Mario Land 2: 6 Golden Coins will play

The game was to originally feature partners, with the only revealed partner being a Chain Chomp, but they were later removed to focus more on stickers.

To date, this is the only Paper Mario title to not begin in Mario's house. Mario's house never appears in game.

Though he never appears in the plot, Luigi can be seen sitting in the backgrounds of 5 different stages. Using paperize, the player can even pull him off the page where he will run off screen. Every time the player does this, the left-most house in the Decalberg Suburbs will have a humorous newspaper article about Luigi being spotted in that location. If the player finds him all 5 times he will appear leading the parade during the credits.

If you tilt the 3DS at any time during gameplay, the shiny stickers on the touch screen will shimmer, like real stickers.

A segment of the Snifit or Whiffit minigame music uses the same tune as the Super Mario Bros. 3 Toad House Minigame.