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.
On Windows WinPDFprint is the simpler way to print your PDF archive or part of it. You can select PDFs and create a list or directly import a list and schedule when to print them on the default printer.