An upcoming firmware update to the 3DS software is set to introduce brand new menu themes. The menu themes are only cosmetic, but they will feature custom icons, folders, background art and even music and sound effects. There will also be a new Themes Store in the eShop where you can purchase new themes. The firmware update is set to release in October.
Nintendo also announced that the New 3DS will also allow players to place face plates on the handheld to better customize the system. Many face plates also have a matching menu theme that can be downloaded from the store.