We recommend that you follow the trunk/branches/tags paradigm for your module folder from the beginning, however, if you need to change from a flat structure to a full structure, here are the steps:
1. Move module to .tmp folder
$ svn mv http://svn.openmrs.org/openmrs-modules/foobar http://svn.openmrs.org/openmrs-modules/foobar.tmp \
-m "foobar: re-organizing module folders"
2. Recreate module folder
$ svn mkdir http://svn.openmrs.org/openmrs-modules/foobar -m "foobar: re-organizing module folders"
3. Move module into trunk subfolder
$ svn mv http://svn.openmrs.org/openmrs-modules/foobar.tmp http://svn.openmrs.org/openmrs-modules/foobar/trunk \
-m "foobar: re-organizing module folders"
4. Switch local copy to trunk
$ svn sw http://svn.openmrs.org/openmrs-modules/foobar/trunk localcopy