From the Super Mario Wiki
An Orange Cube is an item found in The Subspace Emissary of the game Super Smash Bros. Brawl. The cubes contain valuable items and will not reappear once the player gets them. Finding the boxes and getting their treasures is another way to increase the clear percentage.
Also, items that are different from orange cubes occasionally appear — these also affect the clear percentage too. Blue Cubes also appear and are more common and they contain items and occasionally Stickers.
If the player does find a orange cube, the level they found the cube will have a flag above.