Abstract: In an earlier paper (math.SG/0101206), we introduced Floer homology theories associated to closed, oriented three-manifolds Y and SpinC structures. In the present paper, we give calculations and study the properties of these invariants. The calculations suggest a conjectured relationship with Seiberg-Witten theory. The properties include a relationship between the Euler characteristics of these theories and Turaev's torsion, a relationship with the minimal genus problem (Thurston norm), and surgery exact sequences. We also include some applications of these techniques to three-manifold topology.