pdfcrypt allows you to encrypt a PDF (40 bits and 128 bits), set permissions, add user and owner password.
For example you can encrypt a pdf without to allow to print it. The button to print the file will be disabled in Acrobat Reader application.
For example you can encrypt a pdf allowing the user to read it only if he know the correct password
It’s simple to use it like a batch application to set permissions to every PDF in your archive.