Question: Is it possible to encrypt a single directory (or a group of directories) on a Mac? I don't mind if I have to use third-party software.

Answer: 
another third party solution is [truecrypt](http://www.truecrypt.org/). I use it with OS X, Ubuntu and Windows.

TrueCrypt is open source.
For a third party solution I would recommend PGP whole disk encryption
<http://www.pgp.com/products/wholediskencryption/index.html>