I've got a desk full of USB flash disks that I'm prone to lose. I don't care too much about losing the hardware--most are small freebies from tradeshows. But I do care about the data. Here's how to use TrueCrypt to create an encrypted area on a drive. It's like buying a fancy, off-the-shelf, encrypted USB thumb drive, but with a little more hassle and less cost. Now my data stays protected even if lost.
First format a USB flash disk if desired; I like to start fresh. (Right-click the disk, and pick Format.) Install TrueCrypt to the USB drive. (Keep things neat by installing it within its own folder.) Open TrueCrypt, and pick Create Volume. Leave the first option, Create an encrypted file container selected, and pick Next. Choose the Standard TrueCrypt volume, and click Next. Navigate to the root of the USB flash drive, and type a file name that will house the encrypted items. Click Save.
Pick Next. Leave AES encryption and pick the Whirlpool hash. Click Next. Enter the amount of space you want available for encrypted items, and click Next. Enter a password and click Next. Follow the final prompt, and click Format.
Open TrueCrypt to mount the encrypted area. Choose Select File, pick the encrypted file area, and click Open. Highlight an unused drive letter, then click Mount. Enter the password, and Windows will mount the encrypted area to that letter. Just be sure to click Dismount in TrueCrypt before yanking out the drive.