Do you want a free/open source application that can combine, split, rotate, reorder, watermark, encrypt, sign, and otherwise tweak PDF files?
If sure, please have a look jPDF Tweak.

With jPDF Tweak, you can use it to make printable booklets from your PDFs, to add PDF bookmarks, effects (page transitions), to combine multiple PDF files, to watermark them, to rotate pages that do not fit, to attach files to your PDF, to encrypt and sign your PDFs, to change metadata (like author or keywords), and much more.
jPDF Tweak uses the excellent iText library for manipulating PDF files, and JGoodies Forms for the GUI.

JSignPdf is a Java application which adds digital signatures to PDF documents. It can be used as a standalone application or as an Add-On in OpenOffice.org. JSignPdf is open-source software and can be freely used in both private and business sectors.
The main features are,
* several different keystore types (as provided by Java)
* adding digital signatures to PDFs
* setting certification level
* PDF encryption and setting rights
* adding signature icon to PDF (visible signature)
* comprehensive Swing GUI
* support for batch processing (controlled by command line arguments, without GUI)
for details, please visit here.

pdfsam is an open source tool (GPL license) designed to handle pdf files. It requiers a Java Virtual Machine 1.4.2 or higher and it’s released in 2 versions, basic and enhanced.
pdfsam basic:
A simple tool designed to split and merge pdf files. With it’s simple and intuitive interface you can:
* split your pdf documents (into chapters, single pages, etc.).
* merge many pdf documents or subsections of them.
* extract sections of your document into a single pdf document.
* mix alternate pages taken from two pdf documents in straight or reverse order into a single document.
* save and load your environment to automatize your recurrent jobs.
* manage pdfsam settings and set an environment to load at start up.
pdfsam enhanced:
This is the enhanced version of pdfsam. In this version you’ll find all the basic features plus:
* encrypt your pdf files (RC40 bits, RC128 bits, AES128 bits) and set permissions on them.
* add a pdf frontpage or an addendum (or both) to your pdf documents.
* decrypt pdf documents.
* extract attachments from your pdf documents.
* set viewer options to a document to tell the viewer application how should open the document.
for details, please visit here.