JAVA Patching

JAVA is a very difficult program to manage in the enterprise. It seems to have its share of vulnerabilities. Multiple branches continue to be used (1.3,1.4,1.5,1.6). Its not a matter of upgrading to the latest version and removing everything else.
Applications may be hard coded to use a specific version and will break if you uninstall. Since in most cases we did not provide the JAVA, the administrators don’t know in which instances old JAVA is required.
SUN recommends keeping older versions of the JAVA Runtime Environment (JRE) on your system.
Then there is this later articlewhich says with 5.0 Update 6 and later installed on the Windows platform, all applets are executed with the latest version of the JRE. I wonder how the applications hard coded for earlier verions of JAVA would continue to work?
I notice that my vulnerability scanner detects the older versions of JAVA even though a newer version is installed. I’m trying to figure out whether I need to remove these earlier versions to be safe. Even then do I dare remove them if earlier versions are needed by my users.