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The working title for the GameCube was the Dolphin. As a result, many games from the GameCube era reference this, such as Super Mario Sunshine's setting being in the shape of a dolphin (the island is also named Isle Delfino; "Delfino" is Italian for "Dolphin") and Captain Olimar's ship in Pikmin being named the S.S. Dolphin. The GPU of the machine is named "Flipper", another reference to the console's codename.
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Attachment The soft reflections used for the GameCube's startup animation and menu are the same texture file that Ocarina of Time and Majora's Mask use for shiny items.
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There are two hidden alternate start-up sounds which can play after you power-up the console. The first one features a squeaking sound and a child's laughter, which plays when you have a controller in port 1 with the "Z" button hold down as you power-up. The second is of Japanese instruments played which activates via the same method but instead with four controllers.
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Attachment There is a microscopic image of a Dolphin within a computer chip inside the GameCube, referencing the GameCube's codename during development.
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The GameCube's BIOS menu has slow, seemingly random ambient background music.

This background music, when sped up to sixteen times its normal speed, is actually the intro jingle for the Famicom Disk System, a Famicom add-on released by Nintendo in 1986.
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Attachment Among the files uncovered in a massive 2020 breach of internal server data from Nintendo are documents surrounding Project BB2, a never-released, iQue-branded version of the GameCube for the Chinese market. According to an executive summary from January 30, 2004, this system would've played games off of CD-ROM and DVD-ROM discs rather than the GameCube's proprietary format; consequently, it also would've been compatible with audio CDs and DVD video like the Panasonic Q. Project BB2 was also intended to feature karaoke support, owed to karaoke's high popularity in China.
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Attachment At Spaceworld 2000, after Shigeru Miyamoto showed off a tech demo for a GameCube controller prototype he revealed another variant of the Gamecube controller called the "Wavebird". This Wavebird prototype design looked like a missing link between the design of the Virtual Boy controller and the GameCube controller, having long and slender handles like the Virtual Boy but being much bulkier everywhere else like the GameCube controller. It did end up matching the final design of the default GameCube controller.
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In the GameCube 20th anniversary VGC interview, it was revealed that former Nintendo of America VP of marketing Perrin Kaplan thought that there was one aspect of the GameCube that he and NoA were not fond of and made them extremely nervous about the console's perception:

"We actually suggested that the purple was not the best [console color] to start with and [Japan] said, ‘no, we’re going to use that [...] Then we pushed for black and silver, because I think in the US nobody had ever really done the purple colour before. [...] It wasn’t that you couldn’t bring out hardware that was a different colour, it was just a very… ‘female’ looking colour. It just didn’t feel masculine, I think. I remember us being very nervous at E3 that we were going to get bad press purely based on the colour.”

Nintendo of Europe was not to easy on the color either with the company's veteran Shelly Peirce revealing that one person referred to it as a "Fischer-Price record player". However Pierce remained optimistic because he felt that what Nintendo was doing was uniquely different than the competition.
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In an interview with VGC for The GameCubes's 20th anniversary, veteran Rare developer Martin Hollis revealed that not only was he among the first people to see "Project Dolphin", but also that he was possibly responsible for the GameCube's name and theme:

“I arrived in Kyoto, went into the big building, and Mr. Miyamoto and his team straight away took me to this empty meeting room and sat me down in front of a television [...] They switched it on, and Miyamoto told me to press the A button on the controller. I pressed it and the purple rolling cubes appeared on screen with the boot up music that we now know so well, revealing the GameCube name. [...] As the on-screen reveal happened, Mr. Miyamoto stared at my face intensely! That was my initiation, which was maybe because I’d actually suggested the name ‘Cube’ during my time at NTD. Months earlier I did a sheet of paper at Nintendo of America with a whole load of suggestions for names and one of them was ‘Star Cube’ or something like that.”

Nintendo did indeed trademark "Starcube" lending more legitimacy to Hollis' suspicion.
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Attachment The GameCube is technically not a cube. Its dimensions are 5.9 x 6.3 x 4.3 inches, making it more of a rectangular prism.
subdirectory_arrow_right Pokémon Channel (Game), Super Smash Bros. Melee (Game), Super Smash Bros. (Franchise), Pokémon (Franchise)
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Attachment The trophy representing Meowth in Super Smash Bros. Melee is a reference to his appearance in a tech demo shown off at Spaceworld 2000 called "Meowth's Party", which itself was based on a recurring ending musical number from the Pokémon anime. In his trophy he is holding the same red guitar that he performs with in the tech demo. The flavor text for his trophy even directly mentions this tech demo:

"This...is Meowth's dream. Meowth strides all over the globe, scattering invitations to other Pokémon, insisting they come to "Meowth's Party." At this wonderful party, guests are packed in like sardines as Meowth climbs up the stage with its faithful guitar. It strikes a chord, pauses, and then rocks their world!"

A version of Meowth's Party eventually made its way into the GameCube release of Pokémon Channel.
person Wolfen50 calendar_month September 6, 2023
Spaceworld 2000 Meowth's Party tech demo:
https://www.youtube.com/watch?v=62O2vFfS_Ok?t=1387

Pokémon Channel Meowth's Party:
https://www.youtube.com/watch?v=8DcqH7Cl9MY

Meowth Trophy image:
https://www.ssbwiki.com/File:Meowth_Trophy_Melee.png

Original Pokémon anime short:
https://vimeo.com/267748188
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