At one point, the parrot below Creepy Steeple might say "Shine get! Shine get!", a reference to the phrase in the Japanese release of Super Mario Sunshine.

One of the crows in Twilight Town talks about opening a real estate website called "Luigi's Mansion," but his friend warns him against possible copyright infringement.

Lord Crump's theme has the sound of Pac-Man (Atari 2600) dying mixed into it.

A small toad in Petalburg will rave about his favorite video games. First he will talk about Fire Emblem for the Game Boy Advance. Later he'll be talking about Paper Mario for the Nintendo 64. Finally, he'll tell you that he's playing Paper Mario: The Thousand-Year Door itself, and states that the ending is worth playing the game all the way through.

The house in the back alley of Rogueport's main square originally had a toad-shaped chalk outline and dried blood on the floor. These signs of violence were removed from the U.S. version of the game.

In the German version, the Snow World is called "Großfrostheim" which translates into "Great Frost Home". This, however, is a reference to the German city "Großostheim", which is where the Nintendo of Europe headquarters are located, and where the game was localized.

In the Spanish version, Rawk Hawk is named Hawk Hogan as a reference to Hulk Hogan.

After Paper Mario: The Thousand-Year Door's announcement in 2003, some Mario fans incorrectly believed that the character of Madame Flurrie was going to be the ghost of Bowser's wife, based off of her character design and Japanese name. This is due to Flurrie's Japanese name, "Cloudia", sounding a lot like "Clawdia", a popular urban legend name for the Koopalings' mother supposedly created by the Mario fan website "Lemmy's Land", as well as Flurrie sharing a hair style with Ludwig and lip-shape with Wendy, who were at the time considered Bowser's children by Nintendo.

On June 12, 2008, the film studio Morgan Creek Productions filed a lawsuit against Nintendo of America, alleging that Hans Zimmer's song "You're So Cool" from the 1993 film "True Romance" was used in a commercial for Paper Mario: The Thousand-Year Door without permission.

Six days later, Morgan Creek dropped the lawsuit without comment. Nintendo would later release a statement revealing that the day before the lawsuit was dropped, Leo Burnett, their advertising agent, gave Morgan Creek "a copy of a music license entered into between Leo Burnett USA, on behalf of Nintendo of America and Morgan Creek, for licensing of the song."

At one point, the W Emblem was going to be purple. This would imply that when Mario equips the W Emblem, it was originally going to make Mario’s clothes transform into Waluigi’s clothes, as opposed to this happening by equipping the L and W Emblems in the final game.

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.

The gender identity of the party member Vivian is inconsistent between different language translations of the original game. In the Japanese version, Vivian identifies and presents as female, but is described by other characters in the game as actually being an effeminate-looking male, aligning with common media depictions of transgender or gender non-conforming characters at the time, but not explicitly referring to Vivian as such. A rough translation of the Japanese text for Vivian as a party member reads:


The French version directly carries this over and additionally describes Vivian as a boy pretending to be a girl, while the Spanish version describes Vivian as a boy who looks like a girl. However, according to former Nintendo of Europe translator Pol Roca, Vivian's Spanish name "Bibiana" was intended to be a reference to the Spanish transgender actress Bibiana Fernández, who starred in the 1977 film Cambio de Sexo (or Sex Change).

The English and German versions remove any references to being transgender or gender non-conforming, implicitly portraying Vivian as a cisgender woman with "a bit of an inferiority complex". Instead of being bullied over her biological sex, her sisters instead belittle her for her appearance.

The Italian version of the game on the other hand explicitly depicts Vivian as an openly proud transgender woman, with the localization reconfiguring her relationships with gender identity and her sisters by having Marilyn and Bedlam's bullying being rooted in jealousy, traits which are absent in the Japanese script:


The English release of the Nintendo Switch remake follows the Italian version of the original game in unambiguously describing Vivian as a transgender woman, most prominently featuring a line where Vivian states that "it took me a while to realize that I was [Marilyn and Beldam's] sister... not their brother." It's currently unknown if Vivian's portrayal in other translations of the remake has changed from the original release.