The sprites of Geno's star form when possessing the Geno doll and those seen at the end of the game are vastly different, the former being a small, white, almost realistic star while the latter was a yellow, more traditional Mario star surrounded by yellow dots. Similarly, the sprites of the Geno doll when playing with Gaz and the one sitting pose of it seen at the end of the game are proportionally inaccurate to each other.

In the Japanese version, Bowser's Haiku was instead a free-verse poem, which translated to "Why does everyone say 'Mario, Mario'? My heart is very sad", with his name at the end (as a sort of signature) instead of "Haiku".

Looking into the coding of the game reveals several unused enemies (most of which seem to be unused sub-species).

In the Japanese version, Geno's real name comprises of, in half-brackets, several symbols exclusive to the scene where he introduces himself. The symbols in the localized versions are used freely throughout the game in all versions.

Most of the bosses that Mario and his team must fight for a Star Piece are weapon based:
• Mack rides a pogo stick in the shape of a large throwing knife.
• Bowyer is a large, anthropomorphic bow who fires anthropomorphic arrows.
• Punchinello is a large, anthropomorphic bomb who utilizes Bob-Ombs in combat.
• Johnathon Jones wields a trident, and Yaridovich is a large, anthropomorphic spear who also wields a spear.
• The Axem Rangers wield axes and comandeer the Blade, a ship in the shape of a battle axe's blade.
• Smithy wields a giant hammer.

Note that with the exception of Punchinello and Johnathan Jones, all of these bosses are members of the Smithy Gang, the group of antagonists of the game; these allusions to weapons reference Smithy's goal to fill the world with them.

The Axem Rangers (known as kajiā sentai OnoRenjā in Japan) are a parody of the Super Sentai series.

An early screenshot suggests that Luigi may have originally been planned to have more of a role in the game than just cameos.

Bowser's victory pose was changed when it was brought to the U.S. as it previously resembled the "Up yours!" gesture.

In Booster's Tower, there is a room with two curtains. If you go behind one of them and come out the other, Mario will turn into his original 8-bit sprite. You will turn back once you try to exit.

There is a optional hidden boss in Monstro Town named Culex, who is an homage to the Final Fantasy series. His appearance purposely breaks the style in Super Mario RPG to reinforce this homage.

To fight Culex you must go to Moleville and purchase fireworks, then trade them at the little mole's Pur-Tend Store for the Shiny Stone. Use this stone on the sealed door in Monstro Town. You'll end up in a battle with Culex, and if you beat Culex you'll get the Quartz Charm.

Culex's battle, victory, and post-battle conversation themes are (respectively) the boss theme from Final Fantasy IV, the victory theme from the Final Fantasy series, and the Final Fantasy main theme. Also, the Elemental Crystals that Culex uses are the same as in Final Fantasy and Final Fantasy IV.

Models of a Star Fox Arwing and two F-Zero racecars sit atop crates in the back corner of Hinopio's Shop.

The characters Link from The Legend of Zelda and Samus from Metroid can be found inside inns.

When you try talking to Link in the Rosa Inn, the "Puzzle Solved" jingle from The Legend of Zelda series plays. When you try talking to Samus in the Mushroom Kingdom Castle, she claims to be "resting up for Mother Brain".

In Princess Toadstool's room in Mushroom Castle, looking behind the fireplace results in finding a mysterious item labeled "Toadstool's ???". It is never revealed what the item is, as finding it will result in either Toadstool's grandmother driving you away and giving you something else in exchange (the latter one being only on the first instance), or Toadstool angrily scolding you if you have her in your party. In the Japanese version, the item is labeled "Peach's XXX" (as Toadstool is called "Peach" in the Japanese version), giving less subtle ideas on what the item was originally intended to be. As a testament to being one of the Mario series' most famous dirty jokes, "Toadstool's ???" (now renamed to "Peach's" internationally) and the more risqué "Peach's XXX" would both be retained in the game's 2023 remake.