Refrigeration

Because cold air goes down, and cold air is made in the freezer.

It's more efficient that way.

That does seem to be the most common, but there are also side-by-side and freezer-below refrigerator/freezer combinations.

Even at some small loss of efficiency, I would prefer the freezer part below.

The freezer portion of the fridge is used to cool the lower section (in your over / under configuration) by means of a temperature controlled door between the freezer section and the cooler section. Many times you may have noted the rectangular section running vertically down the center of the cooler section. This is being used as a duct for colder air from the freezer. In this type of refrigerator the mechanical refrigeration is only being done in the freezer compartment.