We apply our recently developed theory of frequency-filtered and time-resolved N-photon correlations (del Valle et al 2012 Phys. Rev. Lett. 109 183601) to study the two-photon spectra of a variety of systems of increasing complexity: single-mode emitters with two limiting statistics (one harmonic oscillator or a two-level system) and the various combinations that arise from their coupling. We consider both the linear and nonlinear regimes under incoherent excitation. We find that even the simplest systems display a rich dynamics of emission, not accessible by simple single-photon spectroscopy. In the strong coupling regime, two-photon emission processes involving virtual states are revealed. Furthermore, two general results are unravelled by two-photon correlations with narrow linewidth detectors: (i) filtering-induced bunching and (ii) breakdown of the semi-classical theory. We show how to overcome the latter in a fully quantized picture.