Recent experimental observations of collective excitations of Bose condensed atomic vapours have stimulated interest in the microscopic description of the dynamics of a Bose-Einstein condensate confined in an external potential. We present a finite temperature field theory for collective excitations of trapped Bose-Einstein condensates and use a finite-temperature linear response formalism, which goes beyond the simple mean-field approximation of the Gross-Pitaevskii equation. The effect of the non-condensed thermal atoms we include using perturbation theory in a quasiparticle basis. This presents a simple scheme to understand the interaction between condensate and non-condensed atoms and enables us to include the effect the condensate has on collision dynamics. At first we limit our treatment to the case of a spatially homogeneous Bose gas. We include the effect of pair and triplet anomalous averages and thus obtain a gapless theory for the excitations of a weakly interacting system, which we can link to well known results for Landau and Beliaev damping rates. A gapless theory for trapped systems with a static thermal component follows straightforwardly. We then investigate finite temperature excitations of a condensate in a spherically symmetric harmonic trap. We avoid approximations to the density of states and thus emphasise finite size aspects of the problem. We show that excitations couple strongly to a restricted number of modes, giving rise to resonance structure in their frequency spectra. Where possible we derive energy shifts and lifetimes of excitations. For one particular mode, the breathing mode, the effects of the discreteness of the system are sufficiently pronounced that the simple picture of an energy shift and width fails. Experiments in spherical traps have recently become feasible and should be able to test our detailed quantitative predictions.