pdftk

If PDF is electronic paper, then pdftk is an electronic staple-remover, hole-punch, binder, secret-decoder-ring, and X-Ray-glasses. Pdftk is a simple tool for doing everyday things with PDF documents. Keep one in the top drawer of your desktop and use it to:

• 
  Merge PDF Documents
  
• 
  Split PDF Pages into a New Document
  
• 
  Rotate PDF Pages or Documents
  
• 
  Decrypt Input as Necessary (Password Required)
  
• 
  Encrypt Output as Desired
  
• 
  Fill PDF Forms with FDF Data or XFDF Data and/or Flatten Forms
  
• 
  Apply a Background Watermark or a Foreground Stamp
  
• 
  Report on PDF Metrics such as Metadata, Bookmarks, and Page Labels
  
• 
  Update PDF Metadata
  
• 
  Attach Files to PDF Pages or the PDF Document
  
• 
  Unpack PDF Attachments
  
• 
  Burst a PDF Document into Single Pages
  
• 
  Uncompress and Re-Compress Page Streams
  
• 
  Repair Corrupted PDF (Where Possible)
  

Pdftk allows you to manipulate PDF easily and freely. It does not require Acrobat, and it runs on Windows, Linux, Mac OS X, FreeBSD and Solaris.

http://www.accesspdf.com/pdftk/index.html

PDFsam

pdfsam is an open source tool (GPL license) designed to handle pdf files. It’s released in 2 versions, basic and enhanced.

Requirements:

pdfsam branch 1: Java Virtual Machine 1.4.2 or higher
pdfsam branch 2: Java Virtual Machine 1.6 or higher

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.
• rotate pages of the selected pdf documents.
• visually reorder pages of a selected pdf document.
• visually compose a document dragging pages from selected pdf documents.
• 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.
• set the metadata of a document (author, title, subject and keywords).

http://www.pdfsam.org/