Contrary to popular belief, Smithy is not the same of the sword that plunges into Bowser's Keep. The sword is called Exor, and it is actually Smithy's means of transportation and way of linking the two universes. Even a commercial promoting the game got the names wrong.
Due to a falling out between the companies, this was the last game developed by Squaresoft (later Square-Enix) for a Nintendo system for several years. Normal relations between Nintendo and Square would later be restored.
Culex, the boss behind the sealed door in Monstro Town, is said by many to be a character from Final Fantasy IV (II in America). The music in the background during his sequences is also from the Final Fantasy games. With the advent of Final Fantasy II in America, we have learned what most new all along: that was a load of bull. However Culex was indeed meant to share some traits with Final Fantasy final bosses in general. Furthermore, Culex fights with four crystals, which was a major plot point in Final Fantasy IV.
Another cameo appearance is made by Samus Aran, from the Metroid series. She is asleep in the bed at Mushroom Kingdom Castle's guest room after beating Queen Valentina, but before you enter the Barrel Volcano.
There was a big rumor that claimed Luigi was in the game, as a secret character. Many debunked the rumor-but it is true! Luigi makes a wish at Star Hill and leads the Character Parade at the end of the game.
Many of the characters in the game, including Mallow, Geno, and the chief villain Smithy and most of his henchmen, were new characters made up for this game. They have not been seen in another video game since.
Though this game is almost never referenced in other Mario titles, there are a few references. For instance, a Geno doll appears in the Mario and Luigi RPG series, and Bowser sarcastically calls Mario "friend" in Super Mario 64, since they teamed up in this game.
The game does not have a true sequel, even though Nintendo Power once published an article that they were looking for programmers for "Super Mario RPG 2." Most likely, what would have been the direct sequel was used for the Paper Mario and Mario and Luigi RPG series.