PDF Encrypter is the thing you need if you want to encrypt your PDF documents.
PDF Encrypter allows you to set user password as well as Owner Password. Be sure that no stranger can get access to your PDF file. Besides, there is a wide range of user permissions. For example you can permit to copy and print the file but forbid to modify it. Option FillIn allows people to fill in the form but not to modify it in any way. The program also supports batch mode which can encrypt hundreds of PDF files for you automatically.