Metropolis Monte Carlo (MMC) can be a highly inefficient simulation technique when only a small fraction of an energy surface is populated and barriers between low-energy regions are high. In such cases, previous knowledge of the surface (e.g. low-energy conformations of molecules) can be used to preferentially sample the significantly populated regions. In this work we present a new MC method for accomplishing this goal. We term the method JBW for Jumping Between Wells. The JBW procedure operates by locating the various conformations of a molecule and subsequently driving an MMC-like simulation to jump repeatedly between them. Using simulations on 1- and 2-dimensional potential surfaces and on n-pentane, the JBW method is shown to generate ensembles of states that are indistinguishable from the canonical ensembles generated by classical MMC in the limit. Integration of JBW into the recently described MC/SD hybrid simulation algorithm enables rapidly converged simulations of conformationally flexible molecules including cyclic molecules in all degrees of freedom. The new method (MC-(JBW)/SD) gives converged comformational populations at a rate that is essentially independent of the energy barriers between conformations. We use the method to evaluate free energy differences between the conformers of various substituted cyclohexanes and of the larger ring hydrocarbons cycloheptane, cyclooctane, cyclononane and cyclodecane on several widely used potential energy surfaces. Such conformational free energies are compared with simple molecular mechanics steric energies both with and without rigid rotor-harmonic oscillator free energy corrections. In general, we find that assumptions of harmonicity do not lead to good approximations of the actual anharmonic free energies. In the case of cyclohexane derivatives at room temperature, the MC(JBW)/SD method is estimated to generate converged ensembles of all conformations at a rate ~106times faster than methods based on simple molecular or stochastic dynamics.