We review the prospects for probing new physics with neutrino astrophysics. High energy neutrinos provide an important means of accessing physics beyond the electroweak scale. Neutrinos have a number of advantages over conventional astronomy and, in particular, carry information encoded in their flavor degree of freedom which could reveal a variety of exotic neutrino properties. We also outline ways in which neutrino astrophysics can be used to constrain dark matter properties, and explain how neutrino-based limits lead to a strong general bound on the dark matter total annihilation cross-section.