A digital processor-based remote controller of a wireless remote control system includes a small number of manual input devices, such as keys and scroll wheels, and a graphical user interface. The remote controller can have a single scroll wheel with internal push-to-activate switch, and a small display. This configuration minimizes the size of the remote controller, while allowing for a large number of different control commands to be transmitted to the controlled system. In addition, the remote controller can be configured by the user for both right- and left-handed operation.