In Moodle 1.9 there is an extra choice in the Import Course Data screen: Site files used in this course.
I take it to mean that if we select only a certain number of activities / resources for importing e.g. from Course A into Course B, only those course files referenced in those activities/resources selected for import will be imported, rather than the whole bunch of Course files. For example, images or other media linked to in a Lesson, a Quiz, Glossary or other resource.
However, this does not work as expected: selecting Site files used in this course = Yes does not import any course file!