In MOPAC what is calculated is the Heat of
Formation (HoF) for each geometry.
Differences in HoF values correspond to the differences in enthalpy, deltaH. It is often assumed that the differences in entropy can be neglected, and deltaG=deltaH.
If we compare different TS geometries originating from the same reactants, then their relative energies are important; this increases the chance that the above approximation is valid.
The effects of solvent molecules are very important in this context,
as they affect both the enthalpy and the entropy of a system.
packages incorporate solvent models these days (See Chapter 3, paragraph C).