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Rupees are the currency of Mushroom Kingdom Fusion. They come from the Legend of Zelda series, where they served the same purpose. They are very rare, but can be exchanged for very powerful items in Shops.
Rupees are acquired by defeating enemies, found either in the open or in Containers. They are stored separately from coins. The amount that can be carried is also greater than the number of coins, though the exact maximum amount that can be carried is currently undecided. They come in units of one, five, ten, twenty, and fifty. Collecting black Rupees, known as Rupoors, will decrease your amount.
Many enemies drop rupee equivalent currency when killed, each type worth its own value in rupees. These drop items' sprites are generally themed to their enemy's game. For example Mega Man enemies drop bolts, Mario/Wario enemies drop Wario Land 4 coins, Zelda enemies drop rupees, etc. There are also a number of generic money drops that cover loose end enemies while cameoing obscure gaming currencies.