Hi Shmuel: Beyond Compare 3 converts a PDF to text and compares the text. I've heard that it does a better job than Acrobat's comparison tool, which has a tendency to hang and shows you irrelevant things like different page numbers. I've used Acrobat's comparison tool and it can get confused if things get pushed onto different pages. I've also used Beyond Compare 2 and it does a very good job of dealing with deletions. Reorganization is a harder one to catch.
I've also used FrameMaker's native comparison tool, but only for files, but it's pretty good. I just discovered you can compare books, but I didn't try it. My biggest beef with it is that if I compare two structured documents, the resulting comparison file is unstructured. Fei Min Lorente