In the American version of Super Paper Mario, Dimentio insults Luigi by calling his mustache a "shag". Because this term doubles as a vulgar slang term in British English, the line was changed to have Dimentio call Luigi "pushover" in the European version. Similarly, every instance of "spank" was changed to "yell" or "clobber" in the European version.
When going into Francis' password-protected rooms in Chapter 3-4, look on the shelves to find items and characters from Paper Mario: The Thousand-Year Door (2004), including Petuni, Vivian, and all the Yoshi colors.
When Bowser is fought as a boss, he cannot be jumped on normally due to his spikes. However when playing as him, this property vanishes and he is vulnerable to damage from above.
The enemy Fracktail makes a reference to Zelda II: The Adventure of Link (1987). When Dimentio causes Fracktail to short circuit, he says "I am Error", one of the NPCs in Mido Town.
In the German version of the game, Francis the chameleon is named Konrad, a pun on Conrad, which is a popular German PC store.