kakasoft usb security FREE!!! This is a great program that creates a protected section on your usb drive. Plus, it is cross platform (Windows, Linux). It is really secure and it's open source, meaning ! More info at http://www.kakasoft.com/
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i have just made an instructable for that, but its just for mac. for windows, go to these page: http://www.truecrypt.org/
a good software is called "truecrypt". it encrypts entire drives and can also make file containers if you just want to store stuff in it.
search for "pgp drive" in google.
Follow these instructions: http://lifehacker.com/software/thumb-drive/onthefly-encryption-for-your-usb-flash-drive-154465.php
You can try thisbut i dont know if it works
Encrypt the contents with GPG or other encryption software. Take the software with you on the stick if you need to.
Note that doing this can be risky. If using this on public computers or other computers that are often out of your control, there may be keyloggers on the system. A keylogger will compromise whatever encryption you're doing.