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In the game's standard ending (without collecting all 64 cubes and anti-cubes), the music that plays is a distorted rendition of Frédéric François Chopin's Prelude in E-Minor, Op. 28 No. 4.
This reference is also acknowledged near the end of the credits.
Contributed by Kitsune Hawk
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By running many of the game's songs through a device called a spectrogram, several of them contain hidden images at the very end of the track, including QR codes, paintings by M.C. Escher, and a portrait of United States president Harry S. Truman.
Contributed by Kitsune Hawk
A poster at the beginning of the game references the opening of The Legend of Zelda.
Contributed by The-Big-Boss