The title cards for episodes of the Adventures of Super Mario Bros. 3 cartoon have (with one exception) remixes of the game’s map themes playing. Here are all the themes and their variations that appear in the series. In order, they are: Grass Land (5 different variations), Desert Land (2 variations), the underwater level theme (the only instance of a non-map theme playing), Giant Land, Sky Land ground theme, Sky Land sky theme, Ice Land, Pipe Land and Dark Land.
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The “Mario Special Disc July 2002″ was a Japanese Super Mario Sunshine demo disc produced for E3 2002, containing a demo with six playable missions and three video commercials for the game. This track plays in the disc’s main menu, and due to being unique to a piece of official Super Mario Sunshine media, is technically a Super Mario Sunshine song.
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The European release of the NES version of Wario’s Woods has unique music added that is not present in the other releases of the game. Here is a comparison between the boss themes used in the Round Game mode. From 0 to 38 seconds in this track, one loop of the US/Japanese boss theme plays. From 38 seconds onward, the European boss theme plays.

In Super Mario Odyssey, during the two battles against Madame Broode, Mario must repeatedly capture her pet Chain Chomp named Chain Chompikins to deal damage to her. While capturing Chain Chompikins, an extra layer of rhythmic barks is added to the music; this is hard to hear both due to the abundance of sound effects in the battle and the fact that it is not possible to have Chain Chompikins captured for an extended time. Here is a full loop of the battle music with the barking.
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The main mansion theme of Luigi’s Mansion has several different forms: an instrumental one, three different variations of Luigi humming the song (high, medium and low health), a version with ghost sounds, and finally Luigi whistling the song. In-game, these are separate tracks of the same song; they are played simultaneously while all of them are muted except the active one, in order to be able to switch between the forms without having to load music into memory.

Here is how the song sounds with all its tracks active at the same time. Three Luigis are humming the melody while another is whistling.
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The ending theme to Paper Mario Sticker Star has two phases: saxophone-only and saxophone with orchestra. In-game, this is achieved by separating the music into two track: saxophone and orchestra. It is impossible to hear the second track in-game by itself. Here it is isolated.
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Super Mario Maker makes extensive use of multi-track songs in its soundtrack. The Edit themes all consist of 8 tracks playing simultaneously and fading in and out randomly to create a dynamic mix. However, it is not only the Edit themes that use this technique. Every single track playing in the Course World section of the game (Courses, Makers, and all 100 Mario Challenge themes) is actually a separate track of the same song fading in and out as the player changes between the subsections.

Here is the song with all tracks playing simultaneously, which is impossible to hear in-game. Despite being designed to be played separately, the tracks are harmonized with each other.
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The short remix of the Super Mario Bros. 2 overworld theme heard multiple times during introduction/transition segments in the Super Mario Bros. Super Show, isolated from the cartoon’s voices and sound effects.

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The track “Super Brothers” from the 2000 Sega Dreamcast game Jet Set Radio (also known as Jet Grind Radio in some territories) contains oblique references to the Super Mario franchise. According to the game’s composer, Hideki Naganuma, the lyrics are as following:

“Come go the rescue Peach
The super boy
1, 2, 3, 4, 5, 6, 7
He like mushroom
He’s a playin’ in another dimension
Love love love baby
Who are you? What’s your name? Super Brother”
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On October 28th, 2017, the official Nintendo LINE account published an audio file titled “Jump Up, Super Star! Short Version Free Download”. The audio was a 47-second long sample of the background track of the “Jump Up, Super Star!” song from Super Mario Odyssey, with pitch-shifted Toad sound effects overlaid on top of it to resemble singing. The account then revealed that the song was supposed to be sung by Kinopio-kun, the green Toad mascot of the account, and posted a picture of Kinopio-kun dressed as Pauline (seen as the album art on this post). Note that the Nintendo LINE account is operated directly by Nintendo of Japan.
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