Sybrex SpeedPDF Protection Manager Console is a stand-alone, fully automatic command line based tool to deal with encryption and decryption. It can be used to read and write encrypted PDF documents and set their permission flags.
The program’s features are:

ease of use
40 bit encryption
128 bit ecryption
128 bit AES encryption
recursive search for PDF documents.

The following permissions can be set for crypted PDF document:

Permit low resolution printing
Permit the PDF document to be modified
Permit content to be copied
Enable adding or modifying annotations
Enable form filling
Support screen reader devices for the visually impaired
Permit assembling
Permit high quality printing
The program is a must have tool for every individual or company that works with PDF documents extensively.