We review recent developments in the theory of quantum dynamics in ultracold atomic physics, including exact techniques and methods based on phase-space mappings that are applicable when the complexity becomes exponentially large. Phase-space representations include the truncated Wigner, positive-P and general Gaussian operator representations which can treat both bosons and fermions. These phase-space methods include both traditional approaches using a phase-space of classical dimension, and more recent methods that use a non-classical phase-space of increased dimensionality. Examples used include quantum Einstein-Podolsky-Rosen (EPR) entanglement of a four-mode BEC, time-reversal tests of dephasing in single-mode traps, BEC quantum collisions with up to 10 6 modes and 10 5 interacting particles, quantum interferometry in a multi-mode trap with nonlinear absorption, and the theory of quantum entropy in phase-space. We also treat the approach of variational optimization of the sampling error, giving an elementary example of a nonlinear oscillator.