The reverse nonequilibrium molecular dynamics method for thermal conductivities is adapted to the investigation of molecular fluids. The method generates a heat flux through the system by suitably exchanging velocities of particles located in different regions. From the resulting temperature gradient, the thermal conductivity is then calculated. Different variants of the algorithm and their combinations with other system parameters are tested: exchange of atomic velocities versus exchange of molecular center-of-mass velocities, different exchange frequencies, molecular models with bond constraints versus models with flexible bonds, united-atom versus all-atom models, and presence versus absence of a thermostat. To help establish the range of applicability, the algorithm is tested on different models of benzene, cyclohexane, water, and n-hexane. We find that the algorithm is robust and that the calculated thermal conductivities are insensitive to variations in its control parameters. The force field, in contrast, has a major influence on the value of the thermal conductivity. While calculated and experimental thermal conductivities fall into the same order of magnitude, in most cases the calculated values are systematically larger. United-atom force fields seem to do better than all-atom force fields, possibly because they remove high-frequency degrees of freedom from the simulation, which, in nature, are quantum-mechanical oscillators in their ground state and do not contribute to heat conduction.