Methods for time-dependent quantum-mechanical simulations of large polyatomic systems are described and analyzed, and applications to processes in clusters are presented. Two basic methods are discussed: (i) The Time-Dependent Self-Consistent Field (TDSCF) approximation and its generalizations; (ii) The Classically-Based Separable Potential (CSP) approach, and its extensions. At their simplest respective levels, both methods assume separability of the different modes of the system, and describe each mode as moving in a mean field due to the other modes. In TDSCF the effective single-mode potentials are computed quantum-mechanically, in CSP they are obtained from a classical MD simulation that precedes the quantum calculation. For both methods, improvements are available that correct for correlations between different modes, resulting in approaches of good accuracy. Both the TDSCF and the CSP approach make possible calculations for systems of size and complexity that could hitherto not be treated. Algorithmic and computational aspects of the two methods are examined, and it is found that in typical molecular applications the methods are nearly identical in accuracy, but CSP is greatly superior computationally, especially in applicability to much larger systems than TDSCF. Applications of the methods are presented for: (1) Photoexcitation dynamics and spectroscopy of atomic and molecular impurities in large clusters, e.g., for I2(Ar)n. (2) Collision dynamics, energy transfer and state-to-state transitions in atom-cluster scattering, e.g., He + (Ar)n , Ar + (H2O)n. Future research directions are suggested in the light of the algorithmic aspects and the applications.