We have always been fans of Itext – it is a great tool for creating and editing PDF files, there are free and commercial versions, it is regularly updated, and the developers go out of their way to be helpful on the mailinglists.
There is even a new book on IText coming out, written by Bruno Iowagie (the developer who started it all off). You can buy it from Manning in electronic or printed format. We added 2 sample chapters from the old version to our free PDF Viewer plugin for Eclipse, IDEA, NetBeans if you want to get a feel for Itext.
Now it has got a very nice, slick new site. Definitely worth a look at http://itextpdf.com/