One, as it's name suggests, is based on the state, which means that as the part moves through it's lifecycle it may change it's schema. e.g Inwork 1.0 and Release A.0. It is sometimes used in the military but less if at all in commercial environments. It allows the version to communicate something about the maturity of the part.
Filebased version is very useful (defined as an XML file you import) and you can define almost what you need, we used it for example to allow the client to have upper e.g. A.1 and lower case e.g. a.1 versions for engineering and manufacturing parts. This is possible by playing with the OIR and the skipping versions features, best place to look is the Windchill Help itself which is very complete
BR
Simon
