- Remade the Nintendo DS under the fitting title of "Super Mario 64 DS". Released as a launch title in 2004, this game is a complete retooling of "Super Mario 64" from the ground-up, adding 30 new Power Stars to the original game and featuring 4 playable characters (Mario, Yoshi, Luigi and Wario) each with unique abilities and gameplay attributes. Character movement is done with either the D-Pad or the DS's touch screen, and a "run button" is included to make up for the lack of analog control. In addition to a number of new stages being added, most of the pre-existing ones have been retooled in some way with layout changes or new mechanics, and a number of stage missions have been remixed or completely removed in some cases. Other changes include new items and stage obstacles, modified text/dialogue, different camera controls, a detailed map screen for each part of the game, a four-player competitive multiplayer mode, and a collection if minigames made to showcase the DS's touch screen and microphone capabilities.
- The North American and European versions of "Super Mario 64" have several changes from the original Japanese release. Among these are additional voice lines being added for Mario, an entire voiceover being added for Princess Peach (who lacked any voice acting in the Japanese version), the ability to use both "A" and "B" buttons to interact with things (as opposed to just "B" in Japan), and the omission of several glitches such as the ability to collect 999 coins and break the life counter. There are also several graphical and audio differences, such as a different barking sound effect for Chain Chomps and a different painting for Jolly Roger Bay, alongside various other minor changes in gameplay and level design.
- A 1997 re-release in Japan known as the "Shindou Pak Taiou Edition" adds support for the N64 Rumble Pak and contains most of the changes from the international versions. On top of these differences, the "Backwards Long Jump" glitch has been patched in this version, and an Easter egg on the title screen causes the background to change when the "Z" button is pressed. Other minor changes include modified text, Mario automatically facing the screen when grabbing a tree and the line "So long, ey Bowser?" being replaced with "Buh-bye!"
- The European version adds a language select screen (alongside French and Deutsch translations of the fame), slows down some sound effects, and changes the copyright year on the title screen to reflect the regional release date.
- A version of "Super Mario 64" was released in 2003 for the iQue Player, a China-exclusive localized version of the Nintendo 64 which stored games digitally on a flash card and had online connectivity features. Like most other iQue Player ports, this version (which is adapted from the Japanese Shindou edition) is mostly unchanged aside from translated text, an updated copyright on the title screen, and a lack of Rumble Pak support due to the console's lack of rumble support.
- "Super Mario 64" was featured as a part of "Super Mario 3D All-Stars", a compilation of 3D Super Mario titles released for the Nintendo Switch in 2020. This version used is based on the Japanese Shindou edition, meaning all changes from that version of the game are present including Rumble support and the omission of the Backwards Long Jump glitch. Additionally, the game has been upscaled from 240p to 720p, runs at a consistent 30 frames-per-second, uses AI-upscaled textures as well as higher-quality images of artwork/renders such as the HUD icons, and translates the in-game text as well as changing all button icons to reflect the Switch's different control layout. These changes are applied to the game's ROM in real-time as it runs, meaning the ROM present in the game's files is actually just an unchanged version of "Super Mario 64".
- The game was made available to download for the Nintendo Wii in 2006 as a part of Nintendo's "Virtual Console" line of legacy releases. Although this version of the game is identical to the original release(s) (aside from an improved resolution and requiring the Wii Classic Controller or a Nintendo GameCube controller), a defect in the game's emulation system causes a set of moving platforms in the 2nd Bowser stage to gradually move higher and higher into the air (note: the defect was fixed in all preceding Virtual Console releases for Nintendo 64 games, including the re-release of "Super Mario 64" several years later for the Wii U).
- In June 2014, a disk for the 64DD (a Japan-only disk drive peripheral for the Nintendo 64) was found in a thrift store containing an unreleased "Disk Version" of "Super Mario 64", supposedly displayed at Nintendo's Shoshinkai trade show in 1996 as a playable demo. This version of the game is nearly identical to the cartridge version, but features a different, text-only title screen, a variation of the Peach's Castle music, and a defect in Tiny Huge Island that causes the game to crash if player tries to enter the Wiggler hold at the top of the mountain.
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