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 program also has a little room for improvement. You can't open a file directly from the PDF Protector list, for instance, view its properties or anything else. There's no option to mask passwords; they're always displayed. The interface is sort-of resizable, but it doesn't work quite as it should.
These are small issues, though, and for the most part Free PDF Protector works very well. Drag and drop a whole folder of PDFs and it'll have them password-protected in just a few seconds.