Free PDF Protector is a straightforward tool which can password-protect, encrypt and apply various other restrictions to your PDFs (prevent copying, modifying, high-res printing, more).
The program interface is clear, and for the most part works just as you'd expect. Buttons allow you to add individual PDFs or an entire folder. You're able to enter document passwords, select encryption strength (40/ 128-bit) and any preferred permissions, and clicking "Protect" then applies your settings and saves the results.
This worked well for us. There's a good range of permissions you can set (Allow Content Copying, Allow Modifying Contents, Allow Form-Field Fill-in or Signing, Allow Screen Readers, Allow High Resolution Printing, Allow Low Resolution Printing Only, All Document Assembly or Changing, Allow Annotations). The documents are processed speedily, too.
The interface has improved since we first saw the program. You're now able to open a PDF file (or its folder) directly from the PDF Protector list. Passwords are masked by default (although you can view them if required), and the interface is now properly resizable.
Version 3.0 brings "Import Lists of Files to protect feature, ability to execute the application from the command line, minor GUI improvements."