Using Version numbers is a way to show how BIG the change is
For example 2.4.3 may mean version 2 is the major change to the entire system. .4 is a minor update. and the last .3 is a small bug fix to that version. That way its easily recognisable how much has changed between each version.
Having said that I still see many people use dates or SCM revision numbers as version numbers so long as you have some way to track back to supporting release notes and documentation of what was in-scope for that release there is no real problem.