Thanks DH. I guess I didn't turn up that wikipedia article in my searching, all I was finding was the online versions of the man pages. I did go ahead and try using md5deep on a directory, and it told me:
$ md5deep ~/public_html/
md5deep: /rc00/d05/vocab/public_html/: Is a directory
I suppose there's some other way to take advantage of that recursiveness. In any case, I'm only actually hashing strings with these programs at the moment so effectively, I can expect the deep versions to be equivalent to the nondeeps.
Thanks again for pointing me in the right direction.