The basic computer desk is really just a plain table. The lowest common denominator is a flat table surface supported by four equal legs. To save desktop space you can add a sliding keyboard drawer to the bottom of the table. The desk height is generally between 28 and 32 inches, but custom desk designs should be tailored to the person the desk is designed for rather than built to an industry standard.
Cut an opening in the desk surface and place a piece of glass or plastic on top of the hole. Beneath the desk, build a supporting frame that is strong enough to safely support the weight of a monitor and angle the frame at approximately 35 degrees. This tilts the screen towards the user to avoid distracting glare or reflections from the glass covering the hole. A similar design can be used to place the computer speakers out of sight as well; you can use a plastic grill to cover the opening rather than solid glass or plastic.
Build cabinets on either side of the desk that are approximately 1 inch shorter than the desk height. Attach a piano hinge to the front corner of the cabinet where it meets the desk. Lift each cabinet up until it is flush with the desk surface and affix the piano hinge to the desk. This creates a balanced set of cabinets that pivot forward, creating a sort of cockpit feel for the desk when it is in use. The cabinets can be used for a printer, storage and shelf space for CDs or other computer-related materials.
Build a cabinet that is attached to the top of the desk. The cabinet can be closed in, or left as open shelf space depending on your particular needs. Be sure to make the legs of the cabinet long enough to raise it above your work space when sitting at the desk. To increase your visibility at the workspace, add a fluorescent light to the bottom of the cabinet and point it downward to give ample illumination right where you need it most.