  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.
