As a general rule, a Command Cruiser is a Heavy Cruiser which is built from the keel up to perform command functions, primarily including a Flag Bridge and heavier weapons loadout (to assist in the continuing survival of those on the Flag Bridge).
A Battle Cruiser, however, is usually defined as maximizing the Cruiser-class hull (again, from the keel up) for purely military purposes, which may (and often does) include actually extending the hull to allow for more space.
From there, you have your various variants.