Where can I change the default workspace in Eclipse?
If you are talking about changing the working directory for a java program that you launch from within eclipse, then there's a space for that in the run configuration. If you go to Run menu and select "Run Configurations..." then select your run configuration, then on the "Arguments" tab for a Java Application there is a place for you to edit the "Working directory". This alters the current directory that will be used for launching the java program.
See related question Default eclipse working directory if this is what you are meaning.