Spectra of nonlinear waves in infinite-dimensional Hamiltonian systems are investigated. We establish a connection via the Krein signature between the number of negative directions of the second variation of the energy and the number of potentially unstable eigenvalues of the linearization about a nonlinear wave. We apply our results to determine the effect of symmetry breaking on the spectral stability of nonlinear waves in weakly coupled nonlinear Schrödinger equations.