I'd like to add a little to what Dan said about the CVS "prune directories" option. Selecting this option does not delete directories from the server; it only affects the way CVS checks out directories to your local workspace. If you have this option checked, and there is an empty directory, it will not appear (or will be removed) from you workspace the next time you update.
Since this does not affect the server, it means that if somebody else checks out (or updates) the project, the directory will appear if they don't have this option checked too. It's checked by default when Eclipse is installed, (at least in 2.1), but you might want to double-check that everyone on your team has it selected. Otherwise, someone might mistakenly put a file in it, and it will re-appear that next you update.
Contrary to what Dan said, directories are not put in the ATTIC, only deleted files. There is normally no way to delete a directory within CVS. If you *really* want to remove a directory, it is necessary to delete it from the server at the file system level.
BTW, another good source for additional CVS information is the standard reference, "Version Management with CVS" by Per Cederqvist et al., (usually called "the Cederqvist") available for free download at http://www.cvshome.org.
[ July 23, 2003: Message edited by: David Gallardo ]