The color of each of the Shadow Sirens' hats matches the type of their attacks. Beldam's hat is blue, and she has a "Blizzard" attack. Marilyn's hat is yellow, and she has a "Thunder" attack. Vivian's hat is red, and can use a variety of fire attacks as Mario's partner.

Two names, help_A_access, and help_door_access can be found in the game's files. It says "Hah! I'm not telling you my secrets at the show! Wait for the final version!" These were used as an E3 demo and can't be found in the Multi-Game Demo disc for the Gamecube.

The interior of Mario's house in the opening scene contains a full recreation of the bedroom as it was in Paper Mario, even though only the tiniest bit of it is visible in the opening, and this room is never seen outside of a cutscene.

An unused badge named "Trade Off" still exists in the games data. It was very close to being completed, but never saw the light of day. It had its name translated, and works properly. When used in battle, it will say "Rank Up." The player would be rewarded with more star points after the battle, but the enemies would become tougher.

An early Bonetail texture can be found in the game's data. The only difference is that it has a blue eye. In the final game, Bonetail doesn't have a visible eye, only empty sockets.

Though the Excess Express Engineer's name is not known for sure, his autograph seems to read "Carl".

An earlier version of Mario can be found in the game's files. This version has a thinner outline, much softer colors, and a black moustache. This unused design looks similar to his appearance in the original Paper Mario.

The color of the Yoshi that hatches from the egg in the Glitzville Glitz Pit depends on the amount of time that passes between Mario acquiring the egg and the point in the game where it hatches. The Yoshi is always green in official artwork but can also be red, blue, orange, pink, black, and white.

Whenever Mario falls into water, an up-scaled version of his arm texture graphic appears underneath the game area, outside the normal view of the camera. The same textures also appear during a cut scene in chapter 7 when Mario is sent to the moon.

An unused "Coming Soon" image is present in the game's data. Instead of the game's final title, it uses the name "Paper Mario 2".

In the Spanish translation of the game, Chapter 3 "Of Glitz and Glory" is titled "el rey de los luchadores". When translated, this means "the king of fighters", possibly referencing The King Of Fighters series.

Luigi's partner, Screamy, is based on the original design of the Smorgs.

Within the GameCube version's data are graphics for an earlier Vivian design depicting her with a shorter body and a flame on the tip of her hat. Concept art included in the Nintendo Switch remake reveals that the latter trait was part of an early design for all three Shadow Sirens, with Beldam and Marilyn also having a shard of ice and a lightning bolt at the end of their respective hats. This concept art additionally depicts the Shadow Sirens with black skin, which was changed to purple by the time the early Vivian sprite was created.

Bobbery's early design was actually a Soldier, until it changed into a more of a pirate themed appearance.

In the Spanish version of Paper Mario: The Thousand-Year Door, one of Rawk Hawk's lines is slightly changed to "¡Los aficionadillos deberían quedarse en casa jugando Super Smash Bros. Melee!" (translation: "The weaklings should stay home playing Super Smash Bros. Melee!") after having defeated The Koopinator. In all other versions of the game "Super Smash Bros. Melee" is simply replaced with "video games".

Jr. Troopa from the first Paper Mario can be seen flying in the background of a post card from Zip Toad.

In the Japanese version of the game, Peeka wears bunny ears. This was changed to cat ears in the international release, likely to reduce any references to the Playboy bunny.

The English, French, Spanish, and Italian names for chapter 4 are referencing the Ernest Hemingway novel, For Whom the Bell Tolls.

At the end of the game, the Spoiler:Shadow Queen possessed Peach will ask you to join her. If you answer "Become her servant," you will get an instant Game Over.

When riding the Excess Express in chapter 6, you will have to find a diary for Ghost T. Before you leave, he warns you to not read it. If you read it he will come and kill you, giving you a Game Over.