Electron-phonon coupling in semiconductor quantum dots plays a significant role in determining the optical properties of excited excitons, especially the spectral nature of emitted photons. This paper presents a comprehensive theory and analysis of emission spectra from artificial atoms or quantum dots coupled to structured photon reservoirs and acoustic phonons, when excited with incoherent pump fields. As specific examples of structured reservoirs, we chose a Lorentzian cavity and a coupled cavity waveguide, which are of current experimental interest. For the case of optical cavities, we directly compare and contrast the spectra from three distinct theoretical approaches to treat electron-phonon coupling, including a Markovian polaron master equation, a non-Markovian phonon correlation expansion technique and a semiclassical linear susceptibility approach, and we point out the limitations of these models. For the cavity-QED polaron master equation, we give closed form analytical solutions to the phonon-assisted scattering rates in the weak excitation approximation, fully accounting for temperature, cavity-exciton detuning and cavity dot coupling. We show explicitly why the semiclassical linear susceptibility approach fails to correctly account for phonon-mediated cavity feeding. For weakly coupled cavities, we calculate the optical spectra using a more general reservoir approach and explain its differences from the above approaches in the low Q limit of a Lorentzian cavity. We subsequently use this general reservoir to calculate the emission spectra from quantum dots coupled to slow-light photonic crystal waveguides, which demonstrate a number of striking photon-phonon coupling effects. Our quantum theory can be applied to a wide range of photonic structures including photonic molecules and coupled-cavity waveguide systems.