The correct numerical calculation of the resonance characteristics and, principally, the quality factor Q of contemporary photonic and plasmonic resonant systems is of utmost importance, since Q defines the bandwidth and affects nonlinear and spontaneous emission processes. Here, we comparatively assess the commonly used methods for calculating Q using spectral simulations with commercially available, general-purpose software. We study the applicability range of these methods through judiciously selected examples covering different material systems and frequency regimes from the far-infrared to the visible. We take care in highlighting the underlying physical and numerical reasons limiting the applicability of each one. Our findings demonstrate that in contemporary systems (plasmonics, 2D materials) Q calculation is not trivial, mainly due to the physical complication of strong material dispersion and light leakage. Our work can act as a reference for the mindful and accurate calculation of the quality factor and can serve as a handbook for its evaluation in guided-wave and free-space photonic and plasmonic resonant systems.