We examine numerically the three-way relationships among structure, Laplacian spectra and frequency synchronization dynamics on complex networks. We study the effects of clustering, degree distribution and a particular type of coupling asymmetry (input normalization), all of which are known to have effects on the synchronizability of oscillator networks. We find that these topological factors produce marked signatures in the Laplacian eigenvalue distribution and in the localization properties of individual eigenvectors. Using a set of coordinates based on the Laplacian eigenvectors as a diagnostic tool for synchronization dynamics, we find that the process of frequency synchronization can be visualized as a series of quasiindependent transitions involving different normal modes. Particular features of the partially synchronized state can be understood in terms of the behavior of particular modes or groups of modes.For example, there are important partially synchronized states in which a set of low-lying modes remain unlocked while those in the main spectral peak are locked. We find therefore that spectra influence dynamics in ways that go beyond results relating a single threshold to a single extremal eigenvalue.