Shops are objects in the game. A shop contains 3 chambers which are positioned side by side, each one containing a specific/random item and costing money to activate.
When you find a shop, you may only select one of the three items. When you buy an item, the other two disappear and the item you selected is given to you.
Note that if one is using the Artifact of Command, items in shops will drop directly instead of producing a choice box, unless the item in question is random (a question mark instead of an item shape).