The Republic consists of "thousands" of systems. The Wookies on Kashyyyk appear to not be part of the Republic, although allied to it.
The Separatist Union is an alliance including the Banking Clan, Commerce Guild, and Trade Federation and a number of planets not specified in ROTS.
The Galactic Empire, founded at the end of ROTS, consists at this point in time of the planets of the Republic, as well as (presumably) those which had been controlled by the separatists.
There are also neutral systems, in which much of the actual war took place.