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. The first paper of this series focuses on the assumptions about the shape of the disk, the dust opacities, dust settling, and polycyclic aromatic hydrocarbons (PAHs). In particular, we propose new standard dust opacities for disk models, we present a simplified treatment of PAHs in radiative equilibrium which is sufficient to reproduce the PAH emission features, and we suggest using a simple yet physically justified treatment of dust settling. We propose to use line observations of robust chemical tracers of the gas, such as O, CO, and H2, as additional constraints to determine a number of key properties of the disks, such as disk shape and mass, opacities, and the dust/gas ratio, by simultaneously fitting continuum and line observations.