Top: the Sticker Album in Super Smash Bros. Brawl includes a badge from Paper Mario: The Thousand-Year Door, shaped like a red triangle with a fist emblem. The game calls it the “Mega Rush” badge.

Bottom: however, this is incorrect. In Paper Mario: The Thousand-Year Door, this design is used for the Power Plus badge instead. The actual Mega Rush badge can be seen below it in the list, and uses a different design with an orange octagon.
_{Main Blog | Twitter | Patreon | Store | Source: myself, PM:TTYD (GC) and SSBB (Wii) in various emulators}

Top: in Paper Mario, all bodies of water are translucent, allowing details below the surface to be seen (left), except for one: the pool in the Toad Town Plaza, which has a completely opaque surface (right). Note how Sushie cannot be seen at all below the water on the right.

Bottom: the reason why this particular body of water is different can be found in the game’s first reveal trailer, shown at Nintendo Space World in 1997. There, the pool is seen briefly and is shown to have a reflective surface. Since in Paper Mario, reflective surfaces are faked by having a copy of the area be present upside-down on the other side, at some point in development this was removed due to needing to render too many buildings. As a result, there is nothing below the surface of the pool, which is hidden by the opaque water.
_{Main Blog | Twitter | Patreon | Store | Source: 1: myself, Paper Mario (VC) in Wii emulator, 2}

Top: in Paper Mario, walking towards the spring in Luigi’s secret basement from the back and using Kooper’s field ability will result in Mario falling through the floor after bouncing off the spring. If Right and Down is held while Mario is falling, Luigi can be seen for a few frames in the darkness below the house. This is due to the game storing all characters that are not currently used at the coordinate system’s origin position, which happens to be below the room.

Bottom: After this, Mario will land on invisible ground outside the house, enabling all rooms to be viewed simultaneously. The house can be entered again by walking back into bounds.
_{Main Blog | Twitter | Patreon | Store | Source: myself, Paper Mario (NA, N64) in Wii emulator}

A very obscure feature in the Kent C. Koopa fight in Paper Mario that is unlikely to be seen during an average playthough is that if he is knocked over and then attacked with the Spin Smash attack, he will drop a few coins.

Note that the attack needs a badge to be available, Kent C. Koopa is not trivial to knock over, and there is no indication he would drop coins; together, this makes discovering this very unlikely. In addition, this is the only instance of an enemy dropping coins mid-battle in the game, with the exception of Bandits who previously stole Mario’s coins.
_{Main Blog | Twitter | Patreon | Store | Small Findings | Source: video, info by twitter.com user “BBSplat”}

Top: in the prologue of Paper Mario: The Thousand-Year Door, Professor Frankly briefly looks at the Magical Map after it is first activated. For this, he sets the map down on his table. The texture used for this can not be seen in-game clearly due to being at an oblique angle and too far away from the camera, but it shows the Magical Map completely filled out with all locations instead of in the empty state it should be at that point in the story.

Bottom: extracting the texture from the game’s files, we can see it does not match up perfectly with the finished map; instead, it appears to be an early version of it. Here is an animation comparing the two; the clearer image is the map used in-game while the pixelated one is Frankly’s texture. Some of the biggest differences include: no mountains in the Poshley Heights area in the lower right, a much bigger moon and X-Naut base in the top left, and a differently-colored ground in the Boggly Woods in the top middle.
_{Main Blog | Twitter | Patreon | Store | Small Findings | Source: 1, 2}

In Paper Mario, the battle system is programmed in such a way that positive attack modifiers apply to each individual instance of damage being dealt, even if an attack deals damage several times like Bow’s Smack move.

In the Crystal Palace, there are battles where Duplighosts appear alongside Red Magikoopas. If Mario’s current partner is Bow, the Duplighosts will turn into a copy of her. Then, if the Red Magikoopa raises the Duplighosts’ attack, they will be able to deal extremely high amounts of damage due to the modifier applying to each individual slap. Here, we can see the Duplighost dealing 6 damage per smack after 1 power-up, 10 after 2 power-ups, and 14 after three power-ups, making this the most powerful enemy attack in the game.

_{Main Blog | Twitter | Patreon | Store | Small Findings | Source}