Milk crates are designed to be stackable for transport in refrigerated trucks over long distances. This is a plus for the desk construction since one crate turned upside down on the floor instantly forms the base for another upside-down crate to be stacked on top. Milk crates are about 11 inches high, so making two stacks of three milk crates makes a base that is 33 inches high.
Place the milk crate stacks a few feet apart on the floor, depending on the width of the desktop, and then put the desktop on top. A wood board, an old tabletop, a piece of plywood or an old door makes a good desktop. Anchor the desktop to the stacks of milk crates with heavy books or a computer, or even loop a few 1-1/2-inch copper pipe straps --used to anchor copper wires to a wall -- around the plastic grid that forms the bottom of a milk crate. Secure the straps upward and through the crate, to the underside of the desk with screws. This will keep the desktop from sliding off the crates.
Turn the crates on their sides, and stack them this way to make extra storage beneath the desk. The open space of the crates makes functional nooks for books, papers and supplies. Crates stacked on their sides will not latch onto each other, so secure them with strong cable ties tying the stacked crates together -- near the front and back of the crates.
Long before milk crates were constructed of plastic, they were wood, and they were constructed very well -- sturdy enough to contain several gallons of milk in glass containers. For a desk base, these vintage milk crates will provide adequate structural support when stacked two crates high with the open part facing forward for storage. Screw them together with 1-1/4-inch wood screws and a handy drill. Then screw the uppermost side of the milk crate stack into the underside of the desktop with wood screws to secure the unit together as one, solid desk.
Just because you're using milk crates for the base of the desk, it doesn't mean that they have to have a hodgepodge, mismatched look. Transform the plastic surface of the milk crates with spray paint to give the base of the desk a uniform color. Choose a color that blends in with the desktop or one that makes a bold, accenting statement in the room's decor.