In one aspect of the invention, an engine is operated in a skip cylinder engine braking mode. In the skip cylinder engine braking mode, selected working cycles of selected working chambers are deactivated. Other selected working cycles of the selected working chambers are operated in a braking mode. Accordingly, individual working chambers are sometimes deactivated and sometimes operated in the braking mode while the engine is operating in the skip cylinder engine braking mode. Various methods for cylinder control are described, which improve fuel economy, catalytic converter performance, and vehicle NVH characteristics.