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Speaking of EncFS, here is a notification area applet for GNOME that lets you manage EncFS encrypted folders: Cryptkeeper.

Cryptkeeper lets you import or create new encrypted folders, automatically unmount an EncFS folder after a period of time and change EncFS password.

Cryptkeeper is very easy to use: left click the applet and select Import / New EncFS folder, then follow the instructions. The "change password" option is not very intuitive though: you must left click the applet, then right click an encrypted folder and you'll find the option to change the password as well as to delete the folder or get some detailed info:

Cryptkeeper change password

Unfortunately Cryptkeeper lacks any advanced features so if you want to specify the encryption type, etc., use encfs via command line.

Important: if you use Ubuntu 11.04, Cryptkeeper won't show up in the notification area (systray) by default so you must whitelist it. See this post for more info: How To Re-Enable The Notification Area (Systray) In Ubuntu 11.04, For All Applications

Install Cryptkeeper

Cryptkeeper should be available in your Linux distribution official repositories. In Ubuntu, search for it in Ubuntu Software Center or run the following command to install it:
sudo apt-get install cryptkeeper

Cryptkeeper homepage