This article is one of a series that lays the groundwork for a structure and classification theory of second order superintegrable systems, both classical and quantum, in conformally flat spaces. In the first part of the article we study the Stäckel transform (or coupling constant metamorphosis) as an invertible mapping between classical superintegrable systems on different three-dimensional spaces. We show first that all superintegrable systems with nondegenerate potentials are multiseparable and then that each such system on any conformally flat space is Stäckel equivalent to a system on a constant curvature space. In the second part of the article we classify all the superintegrable systems that admit separation in generic coordinates. We find that there are eight families of these systems.