Many important processes in nature are rare events. Familiar examples include conformational changes of bio-molecules, nucleation events and chemical reactions. From an abstract viewpoint, this can be formulated as the problem of navigating a system over its energy landscape. For simple systems, the classical transition state theory provides an effective description for the transition rates of such rare events. For systems with complex energy landscapes, however, the transition state theory is not the most efficient tool. We wil discuss a new theory, the transition path theory, that is more suited for describing transitions in complex systems. We will also discuss the string method for finding transition pathways and transition rates, that has proven to be quite effective for a wide variety of problems. Applications will be presented for simple examples of phase transformation in solids, conformational changes of bio-molecules with explicit solvent and thermal noise induced switching of magnetic thin films.