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Collisions play an important role in many aspects of the physics of musical instruments. The striking action of a hammer or mallet in keyboard and percussion instruments is perhaps the most important example, but others include reed-beating effects in wind instruments, the string/neck interaction in fretted instruments such as the guitar as well as in the sitar and the wire/membrane interaction in the snare drum. From a simulation perspective, whether the eventual goal is the validation of musical instrument models or sound synthesis, such highly nonlinear problems pose various difficulties, not the least of which is the risk of numerical instability. In this article, a novel finite difference time domain simulation framework for such collision problems is developed, where numerical stability follows from strict numerical energy conservation or dissipation, and where a a power law formulation for collisions is employed, as a potential function within a Hamiltonian formulation. The power law serves both as a model of deformable collision, and as a mathematical penalty under perfectly rigid, non-deformable collision. This formulation solves a major problem underlying previous work, where a Hamiltonian framework was not employed for collisions, and thus stability was not ensured. Various numerical examples, illustrating the unifying features of such methods across a wide variety of systems in musical acoustics are presented, including numerical stability and energy conservation/dissipation, bounds on spurious penetration in the case of rigid collisions, as well as various aspects of musical instrument physics.