The mini-game Gnat Attack actually has a series of trophies that are awarded each time the game is beat. While not "unused", it is unlikely most players bothered to (or were able to) play through the game 15 times to collect them all.

There's a set of rather useful features that are, for some reason, disabled by default. However, they can be unlocked via a simple "code" on the title screen by clicking on the "N" in "MARIO PAINT" to start the staff roll and, when "PROGRAMMER NORIAKI TERAMOTO" appears, holding the right button and clicking the "N" again. By doing so, the player will unlock a series of available commands, most of which are utilized through the right button.
The list of (currently known) hidden features are as follows:
• Right-clicking anywhere on the screen will activate Undodog (with a few exceptions).
• Right-clicking on the canvas in the Stamp Editor will sample the pixel color underneath the cursor.
• Four new rotation options are available in addition to the old horizontal/vertical flip options (see screenshot).
• Pressing L + R + Start + Select on Controller 2 will reset the game (code will need to be entered again).

If the player clicks the R in "MARIO PAINT" on the title screen, a sound reminiscent of a baby laughing will play. If the sound is reversed and slowed down by 50%, it will reveal itself as a backmasked voice saying "Nintendo".

On the title screen, pressing the O will turn it into a bomb, which then explodes. After this, a short 19-note melody will play. This is Totaka's song, a song hidden by Nintendo composer Kazumi Totaka in almost all of the games he has worked on.