If organic molecules are to be used as the active component in devices, self-assembly represents the most attractive route to control the geometric structure and therefore part of the device performance. High-resolution scanning tunneling microscopy measurement combined with density functional theory and Monte Carlo calculations are used to study the stability of self-assemblies of molecules with bonding motifs spanning (nearly) the entire range of intermolecular interaction strengths. Our atomistic model reproduces the experimentally observed crystal structures with sub-Ångstrom precision in all cases. In addition, it is able to identify metastable structures through thermodynamic analysis.