The biggest problem I’ve ever had with PDF files is the fact that I don’t own Adobe Acrobat Pro. So when it comes to making multipage designed documents, I’ve either been stuck doing some creative artboard configuration in Illustrator, or stuck “printing” documents (such as from Photoshop, etc.) to PDF and then using a command line script to merge the files together.
I found this nice MacWorld article that discusses some of the newer (or at least new to me) functionality in Preview for OSX, which details some really nice features, including document merging and annotation, as well as some nice formatting features. Looking forward to using this for making designeriffic podcast/mix PDF booklets, multipage Illustrator-formatted resumes, and whatever else.