There are many unused songs and jingles in the game's data. Unfortunately, only two are still on the disk; there are plenty of file names, but no actual tracks to accompany them.

In the Japanese version, Mario and his partners only get fully healed after completing Chapter 1, but they do not get healed at all after completing any of the other chapters. In the international version, Mario and his partners get fully healed for all of the chapters (besides chapter 8) after they are completed.

When tattling a Bob-omb named Fred in Fahr Outpost, Goombella mentions that he isn't very freaky for a Fred. This is a possible reference to the character Freaky Fred from the cartoon Courage the Cowardly Dog.

Winning the in-game Happy Lucky Lottery isn't actually based on luck at all, but on the date from when you bought the ticket based off of the GameCube's internal clock. The prizes are as follow: 4th prize is anywhere between 4 to 10 days, 3rd prize is 25 to 35 days, 2nd prize is 85 to 115 days, and 1st prize is 335 to 395 days. If you change the system's clock to a day prior and went back to talk to Lucky who runs the lottery, he'll know that the internal clock has been messed with. You can either admit to it or lie to not having tampered with it, however you'll need to pay 500 coins in order to reset the lottery, regardless. Daylight savings is not put into account. Buying a new ticket won't actually increase your chances of winning either but will instead reset the days back to 0 from when you bought it.

Both the original GameCube release and the Nintendo Switch remake are rated E by the Entertainment Software Ratings Board (ESRB), but the GameCube version's rating was simply given the descriptor "Mild Cartoon Violence". The remake’s ESRB rating was updated to replace it with the descriptors "Mild Fantasy Violence" and "Mild Suggestive Themes". These "Mild Suggestive Themes" most likely refer to flirtatious dialogue (i.e. "Aren’t you a fine specimen of a man"; "Perhaps if I…grabbed you and gave you a little sugar") and a character with a large chest/exaggerated proportions, referencing Madame Flurrie.

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.

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.

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.

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

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.

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.

When Peach starts up Sir Grodus' computer, the opening sequence featuring is actually the startup animation from the Famicom Disk System. The yellow disk also resembles one of the FDS's game disks.

The enemy character Red Bones' name in Japanese is "Buraddi Honenoko", which translates to "Bloody Son of Bone" (or "Bloody Dull Bones"), which could hint to a Koopa Troopa having met a gory demise, then being resurrected as a Dry Bones, but still had a stained shell.

All of the partners from the first Paper Mario were originally going to make cameo appearances in this game, but were scrapped for unknown reasons. However, Parakarry and Lady Bow do remain in the game, and make appearances at the beginning and in Poshley Heights after completing the game, respectively.

In the X-Naut Fortress there is a changing room. If you drop into the room from the vent above, both you and your partners will turn into 8-bit sprites, with the original Super Mario Bros music playing in the background. You can turn back to normal by exiting the room.

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

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.

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.

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

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.