We propose a set of standard assumptions for the modelling of Class II and III protoplanetary disks, which includes detailed continuum radiative transfer, thermo-chemical modelling of gas and ice, and line radiative transfer from optical to cm wavelengths. We propose new standard dust opacities for disk models, we present a simplified treatment of PAHs sufficient to reproduce the PAH emission features, and we suggest using a simple treatment of dust settling. We roughly adjust parameters to obtain a model that predicts typical Class II T Tauri star continuum and line observations. We systematically study the impact of each model parameter (disk mass, disk extension and shape, dust settling, dust size and opacity, gas/dust ratio, etc.) on all continuum and line observables, in particular on the SED, mm-slope, continuum visibilities, and emission lines including [OI] 63um, high-J CO lines, (sub-)mm CO isotopologue lines, and CO fundamental ro-vibrational lines. We find that evolved dust properties (large grains) often needed to fit the SED, have important consequences for disk chemistry and heating/cooling balance, leading to stronger emission lines in general. Strong dust settling and missing disk flaring have similar effects on continuum observations, but opposite effects on far-IR gas emission lines. PAH molecules can shield the gas from stellar UV radiation because of their strong absorption and negligible scattering opacities. The observable millimetre-slope of the SED can become significantly more gentle in the case of cold disk midplanes, which we find regularly in our T Tauri models. We propose to use line observations of robust chemical tracers of the gas, such as O, CO, and H2, as additional constraints to determine some key properties of the disks, such as disk shape and mass, opacities, and the dust/gas ratio, by simultaneously fitting continuum and line observations.