Occasional Rhythm Heaven Factsさんのイラストまとめ

In a glance you might assume that the moon in the background is the same sprite in both versions, but it is actually around a pixel larger in Ninja. (the transparent version is the Ninja card)

In the files for Rhythm Heaven DS, there exist an unused sprite of the lady from the Tunnel endless game.
It is uh, quite creepy, if you ask me.

In the files for Remix 7 and Tap Trial 2 respectively are alternate versions of the Giraffe, one being a Dragon and one being a Camel

In the files for Rhythm Paradise is an early version of the Air Boarders title screen. The design is similar but not identical. The cutting room floor claims it matches concept art. I've haven't found concept art, if you know of it please send it, it could be a fact goldmine.

According to the Rhythm Tengoku Gold comic, the playable Clappy Trio member is the Conductor in Glee Club. This has lead to fan speculation that Marshal from Rhythm Heaven Fever is the playable Chorus Kid, but this is unconfirmed.