I have been doing massive amounts of PDF analysis lately and found my self utilizing a tool set that I haven't really heard that much about its a framework called Origami it has the standard pdf analysis features with one cool exception called pdfwalker that allows you to step through the pdf and for those looking to preload a pdf with some goodies it supports injection... It's a ruby gems framework so not too difficult to get up and running.  Take a look:  http://esec-lab.sogeti.com/dotclear/index.php?pages/Origami

Software contain nice tools and features, it's really impressive.