I have long been a keen user of pdftk, the PDF Toolkit, but am frequently surprised when people have not heard of it. True, it is a command line tool, but it is easy to incorporate into service menus, scripts etc and doubtless there is a GUI front-end for it somewhere (in fact there is one linked to from the above page).
Clearly a blog post is called for, but, whilst you wait for a post that will never arrive, here is a link to some examples that should open your eyes to what is possible with pdftk.
To get started on a Debian-based system:
$ sudo apt-get install pdftk $ man pdftk