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Frequency-domain solvers are used extensively for modeling arbitrary metal-based terahertz structures. Four well-known commercially available electromagnetic (EM) modeling software packages include HFSS™, CST Microwave Studio®, EMPro, and RSoft. However, there are a number of operational issues that relate to how they can be used to obtain more meaningful and accurate results. Even experienced users of these and similar software packages may not fully appreciate some of the subtle ambiguities in defining boundaries and material parameters for use in THz applications. To this end, a detailed comparative study has been undertaken, in consultation with all four vendors. First, in order to avoid introducing ambiguities, frequency dispersion in materials has to be clearly defined from first principles; in both intrinsic and effective forms. Different frequency dispersion models are then introduced for `metal-like' materials. To act as benchmark structures, conventional air-filled metal-pipe rectangular waveguides, associated cavity resonators and a spoof surface plasmon waveguide have been simulated, using a raft of different approaches; with a view to illustrating quantifiable weaknesses in commercial software packages for simulating arbitrary metal-based THz structures. This paper highlights intuitive and logical approaches that give incorrect results and, where possible, makes recommendations for the most appropriate solutions that have hitherto not been given in Technical Notes.