Concerning CLASSPATH for Java and PATH for UNIX:
I routinely wrap Java programs in a shell script that does
    export CLASSPATH
    CLASSPATH=".........."
    exec java SomeClass $*
I can't put the .jar files in the same place as the Java libraries
because this is a UNIX system and I don't have the appropriate
permissions for that directory, so something like this is needed.

The same thing for other programs.  If a program wants half a dozen
environment variables to be set up, I wrap a shell script around it
and _don't_ make them global global.

The problem is, this approach works with well separated programs
running as separate processes.  It wouldn't work so well with a "sea
of objects".  What works for that?