Research on conjugated polymers for thermoelectric applications has made tremendous progress in recent years, which is accompanied by surging interest in molecular doping as a means to achieve the high electrical conductivities that are required. A detailed understanding of the complex relationship between the doping process, the structural as well as energetic properties of the polymer films, and the resulting thermoelectric behavior is slowly emerging. This review summarizes recent developments and strategies that permit enhancing the electrical conductivity of p- and n-type conjugated polymers via molecular doping. The impact of the chemical design of both the polymer and the dopant, the processing conditions, and the resulting nanostructure on the doping efficiency and stability of the doped state are discussed. Attention is paid to the interdependence of the electrical and thermal transport characteristics of semiconductor host-dopant systems and the Seebeck coefficient. Strategies that permit to improve the thermoelectric performance, such as an uniaxial alignment of the polymer backbone in both bulk and thin film geometries, manipulation of the dielectric constant of the polymer, and the variation of the dopant size, are explored. A combination of theory and experiment is predicted to yield new chemical design principles and processing schemes that will ultimately give rise to the next generation of organic thermoelectric materials.