Equilibrium free energy differences refer to the change in free energy between two states of a system at equilibrium, indicating the spontaneity of a process. This concept is crucial as it helps predict whether a reaction will proceed in the forward or reverse direction based on the thermodynamic stability of the states involved. In the context of fluctuations and non-equilibrium processes, it highlights how systems can temporarily deviate from equilibrium and how this relates to work done on or by the system.