We apply our recently developed theory of frequency-filtered and time-resolved N-photon correlations 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, novel two-photon emission processes involving virtual states are revealed. Furthermore, two general results are unraveled 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 this shortcoming in a fully-quantized picture.