I use fSekrit for encrypting text based data and use Blowfish Advanced CS for file-level encryption (multiple algorithms).
One good feature of Blowfish Advanced CS is that it has a "work with" feature where you can decrypt a file and work with it in an associated application. Then when you're finished with the application, the file is automatically encrypted with the decryption key and any interim files are wiped.
Blowfish Advanced CS canbe found at http://hotpixel.net/software.html
There's also a zip version so no installers needed. I just unzip and put it on my usb drive.
You can select a folder or multiple files to encrypt at once but they'll be encrypted as individual files with the same password.
I haven't yet used Truecrypt but if I do it will be for smaller container files rather than tens of gigabytes or greater containers.