Mario's fourth role-playing adventure sees him return to the colorful world of Paper Mario for the N64. A strange race of creatures are plotting to unlock the secrets of the mysterious Thousand-Year Door and unleash a great terror upon the planet, and only Mario can stop them!
Mario and his friends must once again navigate through many dungeons, conquer many monsters, and solve many mysteries in order to save the world from certain destruction. This time, the adventure truly utilizes Mario's unique "paper" status, with many unique puzzles requiring the crafty origami skills that only a two-dimensional hero has.
The aforementioned video gaming Toad in Petalburg also mentions playing Fire Emblem on his Game Boy Advance. Nintendo's Fire Emblem series has seen several releases in Japan before finally coming to North America in November, 2003.
The character "Ishnail" in Rogueport is a parody of Ishmael, the main character in Moby-Dick.
When Mario and friends arrive on the moon, Goombella recalls how they "put a Goomba on the moon in '69." 1969 was the year the United States sent a man to the moon.
For Whom the Bell Tolls
Chapter 4's subtitle, "For Pigs the Bell Tolls," is a parody of "For Whom the Bell Tolls," the title of a novel by Ernest Hemingway.
Famicom Disk System
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.
Game Boy Advance (SP)
The first time Goombella sees Mario's Mailbox SP, she asks, "Ooh, is that a Mailbox SP? Cool! With the light?" This is an obvious reference to the Game Boy Advance SP's lit screen—its biggest improvement over the original Game Boy Advance.
In the Glitz Pit, the wall-mounted device Mario uses to schedule matches is based on the design of the original Game Boy Advance.
PM:TTYD has two references to Jumpman, Mario's original name.
As Mario approaches the ring for a rematch with Rawk Hawk, the crowd's chant of "GONZALES!!! GONZALES!!!" ends with "JUMPMAN! Wait, who?"
Jumpman is also the name of a badge that increases Mario's attack power by 1, but disables his hammer.
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.
Paper Mario series
Depending on when you talk to him, one of the Toads in Petalburg mentions playing Paper Mario, Paper Mario: The Thousand-Year Door (!), and "sequel" to PM:TTYD (!!).
Super Mario Bros.
The playable levels in Bowser's subplots are all based on levels from the original Super Mario Bros.
Super Mario Sunshine
At one point, the parrot below Creepy Steeple might say "Shine get! Shine get!", a reference to the phrase in the Japanese Super Mario Sunshine.
Super Mario World & Super Mario Bros. 3
When Mario receives a new e-mail on his Mailbox SP, different ringtones play depending on who sent the e-mail. An e-mail from Peach triggers a few bars of the opening music from Super Mario World. When "X" e-mails Mario, the World 6 (Ice Land) map screen music from Super Mario Bros. 3 plays. The fluttery "Castle Clear" tune from Super Mario World indicates an e-mail from anyone else.
Running joke: 8-bit Mario
When Mario falls behind one of the changing room curtains in the X-Naut lair, he emerges as the "small Mario" sprite from Super Mario Bros., and the music changes to the SMB main theme. A similar gag was used in Super Mario RPG and Paper Mario.