Well-balanced and free energy dissipative first- and second-order accurate finite volume schemes are proposed for a general class of hydrodynamic systems with linear and nonlinear damping. The variation of the natural Liapunov functional of the system, given by its free energy, allows, for a characterization of the stationary states by its variation. An analog property at the discrete level enables us to preserve stationary states at machine precision while keeping the dissipation of the discrete free energy. These schemes can accurately analyse the stability properties of stationary states in challenging problems such as: phase transitions in collective behavior, generalized Euler-Poisson systems in chemotaxis and astrophysics, and models in dynamic density functional theories; having done a careful validation in a battery of relevant test cases.