I would like RCS to version control all the files in /var/spool/cron/crontabs/ and any new files that get created there. But it appears from the documentation that you have to supply it a filename and not a directory name.
Can RCS be used to do this? Is there a better tool to use?
If you need RCS-compatible files, but also need to work with directories, use CVS. Otherwise, use a more modern source code management (SCM) system that handles directories the way you want. In some cases, conversion scripts can ease the pain of migrating, of you choose to do so. Examples include svn import and rcs-fast-export piped to git-fast-import.
RCS works on individual files. CVS uses the RCS file format, but also allows you to add directories. However, directories aren't really first-class objects within CVS, and RCS doesn't have the concept at all. Proceed with caution if you migrate to CVS just for directory support when more modern alternatives exist.
If directories are really important to you, you may want to consider moving to an SCM that treats directories as first-class objects. Subversion (svn) and Bazaar (bzr) both treat directories as versioned objects, and may be good choices for you.
Other systems (notably Git) handle directories as part of tree objects, but don't really version them directly. Instead, for practical purposes you can think of directory versioning in Git as something computed from tree and file objects. This usually works fine, but again it may not be what you need for your project.
Your mileage will vary with other SCMs. When in doubt, consult their documentation.