Thermal plasma flows provide a uniquely high specific enthalpy source that is well suited to transformation of matter, often via phase changes. As a consequence, numerous thermal-plasma-based processes have been developed to, for example, destroy pollutants, modify surfaces (e. g. cutting and welding), synthesize nanostructures and deposit functionalized nanostructured coatings. In many cases, departures from equilibrium (both thermal and chemical) occur in regions of such plasmas; for example, in electrode erosion phenomena or in the injection of a liquid into a plasma jet. This paper reviews the treatment of non-equilibrium phenomena in thermal plasma flows, in particular the methods of calculation of the composition and transport coefficients of non-equilibrium plasmas, which are required for modelling the above processes. The focus is on two-temperature plasmas, in which electrons and heavy species are at different temperatures. Methods of calculation of the composition of plasmas both in local chemical equilibrium (LCE) and out of LCE are presented. A comparison of the different methods shows large discrepancies, even assuming LCE. Two-temperature transport coefficients obtained from simplified expressions, from the modified Chapman-Enskog method and from the Stefan-Maxwell relations are presented, as well as examples focusing on the influence of plasma composition. Different methods of calculation of the collision integrals required in determining the transport coefficients are also reviewed. Particular attention is paid to diffusion, in particular to the combined diffusion coefficient method, which simplifies treatment of plasmas in LCE. The method of calculation of the reactive thermal conductivity and the influence of excited states on transport coefficients are also addressed in some detail.