Like many people in an office setting, I deal with PDFs. But I've long given up any notion that they're inviolable; indeed, marking on them, deleting some pages and not others and then rotating the whole bunch 90 degrees is one way the format can be useful. Sometimes I do this on the command line, but here are two graphical interface Linux tools -- one I've been using a while; another I just discovered yesterday -- that made today's office work possible.
The new find was Xournal. Promoted as a hand-writing tool -- which I'm unlikely ever to use -- it serves admirably to "highlight" on a PDF, and does a nice job typing in extra text. Say, to modify a form for an office or congregation so everyone who signs up for a workshop -- assuming there's not an online sign-in! -- doesn't have to write out the same info each time, like name and address of a congregation.
And there's PDF-Shuffler, that allows you to combine (concatenate) files, delete and reorder pages and pivot their orientation. Very handy.
Ubuntu Linux users can get both from the Ubuntu Software Center. Indeed, look there for details rather than the rather plain software project sites.