RAMADDA supports bulk download of files (as well as on the fly 
generation of THREDDS catalogs).  You can zip up an entire directory 
tree for download, preserving the structure.
Hi Heiko,
For example, looking here:
http://motherlode.ucar.edu/repository/entry/show/RAMADDA/RAMADDA+Examples/Gridded+Data?entryid=ab82e95c-0b7a-4608-ac38-92b87dde7a2a
In the file menu there are Zip Folder and a Zip Tree links. Zip Folder 
will zip up the files that are directly under the folder. Zip Tree will 
zip up the entire Folder tree, preserving the directory structure in the 
zip file.
Also under the File menu is a wget script link. This is a generated 
shell script that does a wget of each of the files in the folder.
There is also an experimental embedded ftp server built right into 
RAMADDA. So (if/when it works :-)) you can ftp to ramadda. The folder 
structure (which is really in the database) is made to look like a ftp 
directory structure. So far we haven't implemented mget or pattern matching.
-Jeff