Yume Nikki's game files contain some unused content.
Mars
There is an unused door graphic in the tileset of Mars-san's room. It fits perfectly on one of the walls, but it just isn't there.
FC World C
A huge part of FC World, known as FC World C, is unreachable. There is also a smaller island with four statues that cannot be reached in any way.
Graphics for three different FC world trees exist, but only the one on the right is actually used.
There are six more unused tiles, and they appear to be drawn in a different art style.
Madotsuki's Room
There is a cracked window: 
And a round pillow: 
A sprite for the trash can with paper inside exists, but goes unused: 
Number World
In the tileset, there seems to be an unused object that resembles that of a streetlight. The Number World connects to the Lamp World, which contains many streetlights. This was probably going to be used as the streetlights, but went unused.
Puddle World
A Japanese Torii gate appears in the tileset.
Witch's Island
The pond on Witch's Island sometimes contains some sort of sea creature called Tasei's Kid. If you noclip (preventing Madotsuki from being obstructed by objects) in his pond and interact with him, he will make a strange noise. He can also be stabbed with the Knife effect by noclipping in the pond.
However, it is instead used for when you stab the big Goblin.[1]
It is also used when you interact with one of the NPCs located in Neon World, but it is sped up.[2]
A Scrapped Gate
A purple gate. It was used in previous versions of the game but was removed later on.[3]
The Lost Party Member
Another Party member can be added to your party, but this never happens in the game.
It's nameless and there are no sprites associated with it. But having it in your party causes Several scripts in the game to change.
- All sane and insane Toriningen disappear. The Toriningen Party and the lunatic in the Mall are not removed.
- The top-left cupboard in the Guillotine Room will disappear. If you stand on it's former tile and press the action button, then you will end up in front of one of the eight cupboards in the Number World. If you enter the world again, then the cupboard will have returned to its rightful spot. This works in the bigger version of the Guillotine Room, too.
- If you wake up, you will be unable to move. You can still open your menu.
- The ending is not changed at all.
This party member requirement prevents events that should be "called" from being triggered directly.
Train Passenger
Sprites exist for a train passenger that cannot be found in game.
Buyo Buyo
In the files, there are unused sprites for the Buyo Buyo in a different art style. This could possibly mean that he was never meant to be in a FC World, but rather, one of the main ones.
However, in version 0.06 of the game, it is seen inside of one of the shacks located in The Wilderness. It is unknown why it's main sprite went unused in the first place, as it's sprite is still found in the game files in later versions.
Submarine Fish
There appears to be an unused palette/version of the Submarine Fish hidden in the game's files. This version is lighter and less detailed, and also kind of chopped-off. This could imply that this version was scrapped before it could ever be finished.
The Flower Path
Interacting with the flowers in the Flower Path calls a common event that is meant to play from a sound file named 'flower', but it cannot be played as the file doesn't exist.
The Spaceship
While the ship is not falling or grounded, and before the falling event is triggered, a map event is continuously triggered. This event has a 1 in 41 chance of calling a common event that is meant to play a nonexistent sound file named 'ポーン' in 1 of 4 different pitches.
References