Autonomous navigation (AutoNav) for deep space missions is a unique capability that was developed at JPL and used successfully for every camera-equipped comet encounter flown by NASA (Borrelly, Wild 2, Tempel 1, and Hartley 2), as well as an asteroid flyby (Annefrank). AutoNav is the first on-board software to perform autonomous interplanetary navigation (image processing, trajectory determination, maneuver computation), and the first and only system to date to autonomously track comet and asteroid nuclei as well as target and intercept a comet nucleus. In this paper, the functions used by AutoNav and how they were used in previous missions are described. Scenarios for future mission concepts which could benefit greatly from the AutoNav system are also provided.