Diffpdf Portable 2.0.0 is a PDF comparison tool that shows the differences in PDF files either textually or visually. It's packaged in PortableApps.com Format so it can easily integrate with the PortableApps.com Suite. It supports upgrades by installing right over an existing copy, preserving all settings. And it's open source and completely free.

Features
By default the comparison is of the text on each pair of pages, but comparing the appearance of pages is also supported (for example, if a diagram is changed or if a paragraph is reformatted). It is also possible to compare particular pages or page ranges. For example, if there are two versions of a PDF file, one with pages 1-12 and the other with pages 1-13 because of an extra page having been added as page 4, they can be compared by specifying two page ranges, 1-12 for the first and 1-3, 5-13 for the second. This will make DiffPDF compare pages in the pairs (1, 1), (2, 2), (3, 3), (4, 5), (5, 6), and so on, to (12, 13).

From the author of the program:
I use the tool regularly to compare different versions of my books (which are typically 500 or more pages), e.g., comparing a first printing with a second printing, to make sure that only the pages I intended to change have actually been changed.

Change log 2.0.0
- Can now have comparisons exclude text that’s outside user-specified margins. This feature was sponsored by a company that prefers to remain anonymous.
- Save As can now save images as well as PDFs.
- Minor bug fixes and improvements.
- Command line help (–help) will no longer work on Windows. This is to avoid a spurious console window appearing. I’ve put the output in the online help though.
- Improved dock window handling so that docks can now be stacked on top of each other (useful for small screens).