While the dark matter (DM) paradigm has proven tremendously successful in explaining large-scale properties of the Universe, the exact micro-physical nature of the dark matter particle remains unknown. Simultaneously, discrepancies between collisionless DM simulations and observations at the dwarf galaxy scale have called into question these simplest models and provide an avenue to explore and constrain alternatives. In this talk I will present high resolution n-body simulations of both collisionless and self-interacting dark matter (SIDM) halos. My simulations show that the high mass to light ratio of dwarf galaxies makes their host halos most susceptible to the effects of new dark sector physics, while more massive hosts will be less affected. Furthermore, I show that it is possible to resolve the problems at the dwarf scale with currently allowed SIDM cross sections. Dwarf halos are very sensitive to baryonic physics, however, and I discuss how supernova feedback and reionization impact these results.