It depends on what the mushrooms are to be used for. For stuffed mushrooms, or to use jumbo caps in place of burger bums, I remove the stems. For an attractive presentation in stir fries, and soups, I eave the stems on. If I'm using the mushrooms for flavor, as in a pasta sauce, I roughly chop them. For duxelles, the mushrooms are minced. If they are to be battered, and deep fried, they are left whole.
Like with most foods, different uses call for different treatment of the ingredient.
Seeeeya; Chief Longwind of the North