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We present efficient numerical methods for the simulation of small magnetization oscillations in three-dimensional micromagnetic systems. Magnetization dynamics is described by the Landau-Lifshitz-Gilbert (LLG) equation, linearized in the frequency domain around a generic equilibrium configuration, and formulated in a special operator form that allows leveraging large-scale techniques commonly used to evaluate the effective field in time-domain micromagnetic simulations. By using this formulation, we derive numerical algorithms to compute the free magnetization oscillations (i.e., spin wave eigenmodes) as well as magnetization oscillations driven by ac radio-frequency fields for arbitrarily shaped nanomagnets. Moreover, semi-analytical perturbation techniques based on the computation of a reduced set of eigenmodes are provided for fast evaluation of magnetization frequency response and absorption spectra as a function of damping and ac field. We present both finite difference and finite element implementations and demonstrate their effectiveness on a test case. These techniques open the possibility to study generic magnonic systems discretized with several hundred thousand (or even millions) of computational cells in a reasonably short time.