Mario and Luigi Bowser's Inside Story: Bubble Lake Underwater (Inside Bowser)
Okay, the normal underwater theme has never been used much, and for the life of me I cannot remember if hearing it was ever needed in game, but this version got screwed over far worse. You see, the music changes when you're inside Bowser, correct? Well yes, and here, you'll never really get the opportunity to try this, since the underwater sections require no cooperation at all from Mario and Luigi. Yeah, most will never hear any of this song, and what a pity it is, since it may well be even better than the standard version of the seabed theme:
Donkey Kong Land 2 Rambi Rumble
Also known as 'Run Rambi, Run!' The original version is well known and already quite rare as it is, only played when King Zing chases you in said level, but the Game Boy version just drops the theme outright and only has it accessible from the music test.
What a major pity this is, since like most of the music in the Donkey Kong Land games, this version is an eight bit classic of video game music legend. Ah well, hear it now:
Donkey Kong Land 3 Rocket Run
Wait, what the ***? Rocket Rush isn't a level in the Donkey Kong Land version? No it isn't, but obviously Rare were planning to have it in in, since the game ROM has a version of the Rocket Run theme only accessible via hacking.
Sounds fairly like the original. Presumably, the level never got built/finished because the technical aspects were too much for the original Game Boy to cope with, so Rare just said '*** it' and canned the whole thing (note how it's not the only level never ported to Game Boy, past games had no Haunted Hall, Castle Crush, Kudgel or Belcha). However, since the level sucked, I guess you can be quite happy they never added it to Donkey Kong Land 3 while all the while mourning the loss of fairly decent music.
WarioWare Twisted/Touched: Mona Pizza Theme
This will come as a big surprise to anyone, especially if they live in the USA or Japan. But Europe never got to hear this music until it got a remix in Super Smash Bros Brawl.
Why you may ask? Because Nintendo didn't release WarioWare Twisted, and hence as a result, blocked us from hearing the music in two games rather than one, since Touched requires a copy of Twisted in the DS GBA slot to unlock the music video.
If you ever want a reason to have EU regulations, this is pretty much it. If you want to hear the music:
And the video no one here ever got to see:
But thankfully, here's how to get it if you don't have WarioWare Twisted (presuming you have WarioWare Touched):
Get an Action Replay DS device, start it up, insert WarioWare Touched and enter this Action Replay code:
Now, go into the debug menu, set one part (I think the top option) to MonaPizza or the like, and the other option to Epilogue Test. Then, press A or so to play the microgame, which really just sends you to the video.
I think then you can go back to the main game after watching, click the UFO and you'll get the video to add to the Toy Room.
The toy will then be permanently unlocked on your game cart and you can view it without any AR codes at all.
Super Mario Bros 2 Subspace
It's also possibly one of the most well hidden Easter Eggs/Mario references, because you only get to hear about seven seconds of the song, and fail to often realise that's an extremely well known one's remix.
Indeed, it's actually a deliberate change to the localisation, the original Doki Doki Panic simply has a ten second loop for said areas. If you need proof Super Mario Bros 2/Super Mario USA is more than a graphics swap, note how they added this song and the Star Man song from the original Mario platformer.
Still, what a wasted use of a classic song, considering you get to hear maybe ten seconds of it max.
Super Mario Galaxy 2 Squizzard
Hard choice to make, because Galaxy 2 loves having songs that have no real use made of them whatsoever. You've got the Perfect Run, with a massive FOUR different themes from the original used in just one level, Boss Blitz with it's four different boss themes and one neutral song you'll pretty much never hear and two different songs in the Rolling Coaster Galaxy, one of which is played for maybe the ten seconds where you're not on the star ball.
But Squizzard, is interesting. Not for being a well designed boss, but for having TWO distinct themes in the game, never found again. One is the standard slow paced boss theme, one is the fast paced almost eastern sounding Fire Flower theme unique to this battle. Have a listen:
New Super Mario Bros Wii Second Airship Theme
Huh? Yeah, the slow paced alternate remix found in maybe the single rooms before Bowser Jr is fought. It's not great, but sadly it's heard so little hardly anyone remembers it.
This is the common one I think:
But there's also this slightly weird version:
It's only played below decks in a certain area I think. Probably a good thing though, it competes with Joke's End and the SMB 2 cave music for sheer repetitiveness.
Okay, make the torture stop someone! It'd go well for a song for the ice part of a film based on Dante's Inferno.
Wario Land 4 Golden Passage
Aka the song you'll never hear because the Frog Switch is located right under the entrance vortex. And because pausing stops the music.
Nintendo hates people don't they?
Here, have a quick listen. It's pretty creepy, and honestly, probably better than the 'Get Out!' theme for this point in the game.
This person even shows you how the theme works in the level by using Gameshark to avoid the switch:
Wario Land 4 Ending mixes
Another type of song few will hear, these are only played in the game's ending. You know, the very short snippets of music played as Wario drives home from the Golden Pyramid?
Mario Kart 64 Rarely Heard Ending Theme
Here however is the record for 'hidden' music. You have to wait about FIFTY minutes on the results screen to hear this hidden loop of music, or about the 64th loop of the ending music. Many of the other songs are easy to hear, rare or require hacking, this just requires a ridiculous amount of patience and people thinking you're a crazed lunatic in the process.
Indeed, doesn't even hearing about this sound like some kind of video game urban legend?
Super Smash Bros Brawl Cruel Brawl
True, this isn't technically very well hidden, but boy is it a wasted song. Basically, it's in Cruel Brawl, and that's it. You can't unlock the music or play it on Battlefield at any other time, use it in the Stage Builder without the computer program 'Stage Studio', or listen to it in the Sound Test.
Here's the song:
Which unless you're freaking God, you'll never hear in it's entirety. Those Fighting Alloys are too freaking annoying!
If you want to hear it in game, get this program:
Then make a stage on the computer with the Cruel Brawl theme set as the background music. And transfer it to the Wii console with an SD card.
Tokata's Song, many games
It's pretty much his signature theme for every game he's worked on the music for, and an Easter Egg which a lot of hardcore gamers like to go searching for. In Super Mario Land 2, it's basically hearable 2 and a half minutes after waiting on the game over screen.
And it's in Luigi's Mansion somewhere:
It's also obviously in Mario Paint, Zelda Link's Awakening, Virtual Boy Wario Land, Pikmin 2, Animal Crossing and Yoshi's Story among others. This page has a list of most of the known appearances of said song in Nintendo games