The role of Jacobian factors in free energy simulations is described. They provide a simple interpretation of "moment of inertia correction" and "dynamic stretch free energy" terms in such simulations. Since the relevant Jacobian factors can often be evaluated analytically by use of the configurational partition function of a polyatomic molecule, it is possible to subtract them from the simulation results when they make unphysical contributions. An important case arises in alchemical simulations that use a single topology method and introduce dummy particles to have the same number of atoms in the initial and final state. The more general utility of the Jacobian factors for simulations of complex systems is briefly discussed.