Estimating standard Gibbs free energy of a molecule
You will need to calculate the partition functions for each type of motion and then calculate the thermodynamic quantities from these.

As to internal rotation, if the energy for this is far greater than $k_BT$, such as with a C=C bond, then treat it as a torsion and use this frequency. If the barrier to rotation is small compared to $k_BT$ then treat it as a free rotor but reduce the partition function by n if there are n barriers. In the intermediate case you will have to find the barrier (say by spectroscopy) and fit the data to a model of the potential (usually of a cosine form)and then numerically solving the Schrodinger eqn. to find energy levels. 

If your temperature is so high that cis-trans reaction occurs then you should probably have to treat this as a mixture.