- Merge or Encrypt / Decrypt PDF files using pdftk

Pdftk is a simple command line tool for doing everyday things with PDF documents. Use it to merge PDF documents, split PDF pages into a new document, decrypt input as necessary (password required), encrypt output as desired, fill PDF forms with FDF data and/or flatten forms, apply a background watermark, report on PDF metrics, update PDF metadata, attach files to PDF pages or the PDF document, unpack PDF attachments, burst a PDF document into single pages, decompress and re-compress page streams, and repair corrupted PDF files (where possible).

Installation:
Ubuntu user can install pdftk using following command: sudo apt-get install pdftk

Using pdftk:
Once installed, we can merge pdf files using following command:

pdftk 1.pdf  2.pdf  3.pdf cat output 123.pdf

Encrypt a PDF using 128-Bit Strength (the Default) and Withhold All Permissions (the Default)

pdftk mydoc.pdf output mydoc.128.pdf owner_pw foopass

Decrypt a PDF

pdftk secured.pdf input_pw foopass output unsecured.pdf

source:http://linuxpoison.blogspot.com/2010/07/135781677514681.html