HowTo: Encrypt specific directories (not whole filesystems) in Ubuntu. - Overclockers Australia Forums
** SPECIAL NOTE ABOUT SHARING VIA SAMBA **
If you want to encrypt a directory on your fileserver and have the decrypted mountpoint accessible by Linux or Windows clients via Samba, you need to modify your setup slightly to permit "other" access to the Fuse device.
First, modify the /etc/fuse.conf file so that the last line "user_allow_other" does NOT have a leading hash. Save and exit. You do not need to reboot.
Next, add an option to your EncFS mount command. In the HowTo example, you would use:
$ encfs /home/joeuser/encrypted_data /home/joeuser/decrypted -- -o allow_other
This will permit a Samba share to see and give users access to your decrypted mountpoint as a regular everyday folder.
Note that this option does not give global "other user" access to all your encrypted folders - it gives access on a per-mountpoint basis only. If you setup a folder inside a Samba share with this option and another folder under the same share without it, the first mountpoint will appear as an accessible regular folder (containing decrypted data) and the second mountpoint will appear as an inaccessible file, despite appearing locally as a decrypted folder.