If you want to recreate the homework in the current course for a new course on the same machine you can do the following:
1. export all of the homework sets from course1. This exports the data knowledge about the contents of the homework sets to set definition files stored in course1/templates.
2. create course2 using course1 as the "template" instead of using modelCourse (this has to be done from the admin page of webwork -- a mere instructor can not do this.) This copies over all the files in the templates and html directories in course1 but not the database (that's why you have to export the homework sets first)
3. go to course2 and import homework set definitions (you can import them
all at once)
-- you are now set for the next semester.
In newer versions of WeBWorK there is an Archive link on the FileManager page
that lets you create a snapshot of your course -- all student data included. This can be downloaded for backup or to transfer the course to a machine or to use it again in two years. The .tgz file is created in the template directory and you can download it to your desktop using FileManager.