Linux.com (Slashdot sister site) has a quick look a file encryption using EncFS and Loop-AES as examples before briefly examining other options. From the article: "you can find a number of options for filesystem encryption in Linux exist, depending on your needs. The most important thing when choosing which one to use is to be clear about your needs. Will the size of the files you need to encrypt grow or stay static? Do you need to encrypt certain files or entire partitions? What level of security do you need? Answers to these questions will help determine the most appropriate program to use."