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.

Winning in-game the 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.

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.

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.

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.

Despite Heff T. claiming that he can't get out of his own cabin, he can in fact be seen twice not within it.

There are a series of glitches that will lead to the character Flavio joining Mario's party and never leaving. He will also appear in cutscenes that Mario himself is not even in.

Francesca's name in the Italian translation of the game, Romoletta, paired with Frankie's translated name, Giuliano, makes a reference to Romeo and Juliet, whose love is impossible due to their families rivalry. The name Francesca can also be considered the female counterpart of Frankie, underlining their link.

It's impossible to lose the first battle in the game to Lord Crump. Even if the player enters the fight with only 1 HP due to taking damage from environmental hazards, the game will increase the player's health to five at the start of the fight and only allow the player to attack or defend.

Early designs for Smorgs can be found in the game's files. They look less fuzzy than in their final design.

The ringtone when Peach calls Mario is the title screen music from Super Mario World.

Grodus' dialogue has an error within the game's script. If the player chooses "Don't attack", he will say "WORM! You dare defy me?!?", even though the player is doing what he said. Likewise, if the player chooses "Attack", Grodus simply tells Mario to stop his blubbering. The responses appear to be the wrong way round.

TEC is likely based on HAL 9000 from the movie 2001: A Space Odyssey. Unlike HAL, TEC isn't insane or malevolent. Another Mario series spoof of HAL was HAL 9001 from The Super Mario Bros. Super Show! live-action episode "9001: A Mario Odyssey."

The fact that Ghost T. resides in Room 004 is a reference to Japanese and Chinese culture in which the number four (四; Rōmaji: shi, Pinyin: sí) is regarded as unlucky, as it sounds similar to the word "death" (死; Rōmaji: shi, Pinyin: sí).

Eddy the Mask's name may be based on Eddie the Head, the mascot of British heavy metal band Iron Maiden.

During the battle with Vivian, she can use Fiery Jinx when her HP is low. However, when Vivian joins Mario's party she has to be Super Ranked to learn that ability.

If the player looks through Professor Frankly's trash can after fighting the Shadow Sirens, they can find Vivian's Tattle, but not Marilyn's or Beldam's. This foreshadows that Vivian would join the party, rather than fight Mario again with the other sirens, as only Tattles of one-time enemies can be found in the trash.

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.

An early design for Vivian was much shorter and had a flame on the tip of her hat.

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

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.

In the Japanese and European versions, Vivian is portrayed as the youngest brother (not sister) of the Shadow Triad as a transvestite, with references to his gender identity being retrospectively seen as representative of typical portrayals of transgender people in popular media at the time of the game’s release. A rough translation of the Japanese text for Vivian as a party member reads:

カゲ三人組の一人だった　オンナのコのようで　ホントは　オトコのコ
"One of the shadow group, Vivian appears to be a girl but is really a boy."

This was changed in the English localization to simply make Vivian a girl with "a bit of an inferiority complex."

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.

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.

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.

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.

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.