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The following solution worked well for me in various environments:
sourceDir="some/directory"
targetDir="any/other/directory"
find "$sourceDir" -type d | sed -e "s?$sourceDir?$targetDir?" | xargs mkdir -p
If you can get access from a Windows machine, you can use xcopy with /T and /E to copy just the folder structure (the /E includes empty folders)
[EDIT!]
This one uses rsync to recreate the directory structure but without the files. http://psung.blogspot.com/2008/05/copying-directory-trees-with-rsync.html
Might actually be better :)
Substitute target_dir and source_dir with the appropriate values:
cd target_dir && (cd source_dir; find . -type d ! -name .) | xargs -i mkdir -p "{}"
Tested on OSX+Ubuntu.