Super Mario 64 2, intended for the doomed N64 Disk Drive. It was to star co-op multiplayer, and a playable Luigi, though all what was revealed is a pyramid level screenshot. Even before that, rumors started going around that the original Mario 64 was named at one point Super Mario FX (actually a code name for the FX chip) and was destined to the SNES before being completely scrapped. This was proven to be false though.
Urban Legend of Zelda: The "L is real 2041"/"L is real 2401" plaque on the statue in the castle courtyard's pond (where you can also find the Boos). Despite being very fuzzy, this was commonly interpreted as some way to unlock Luigi (who ended up being playable in the remake).
Then when the DS version came out, everyone thought that since Wario and Luigi were in it, Waluigi had to be a hidden unlockable character.
This message is also thought to say "Eternal Star." Incidentally, Eternal Star would be the final board in Mario Party.
Someone once said that the 2401 refers to the date Paper Mario, which Luigi was in, was released in North America. According to The Other Wiki, however, it was actually released a day later, on February 5th, 2001, but it's close enough, right?
Early previews imply Bowser was going to have the ability to shoot ice from his nose. This would later be given to the robotic Bowser in Luigis Mansion.
32 courses were originally planned, but only 15 wound up in the final game.
A multiplayer function was planned early on, but scrapped, likely due to hardware limitations. Likewise, Luigi was briefly planned to be present in the game, but scrapped due to technical problems.
Originally, the goalposts from the original Mario game were to be featured, but Miyamoto and co. decided it was more fun to have Power Stars as the goals instead.
A scrapped item for the Big Boo's Haunt level included a "Boo Key".
Mario's triple jump in the Beta was slightly different from the final game.
The games code has an unfinished model of a proposed Blarrg enemy, based on the creatures from Super Mario World.
Some of the beta designs for characters (such as the Thwomps, Bomps, the Koopa Shells, Pokey and the penguins) are slightly different from the final game.
While it goes without saying, this game is not even close to being the 64th title in the series. Counting all the "main" Mario games note Donkey Kong, Donkey Kong Jr., Mario Bros., Super Mario Bros, Super Mario Bros. II (jpn, later called The Lost Levels) Super Mario Bros. 2 (USA), Super Mario Bros. 3, Super Mario World and Super Mario World 2: Yoshi's Island and discounting ports and spinoffs, this would likely make Mario 64 the tenth entry in the series. Ironically, counting all of the ports, spinoffs and cameos, the 64th Mario game released would be none other than the arcade port of the original Super Mario Bros, called Vs. Super Mario Bros.