We’ve talked about both WinMerge and DiffMerge in the past, and both are great file comparison utilities. When it comes to comparing files, however, these generally only focus on text-based files meaning PDFs are left out in the dark. There is another free program called DiffPDF that can handle those files for you.
DiffPDF has two different ways it can compare PDF files: by text or by appearance. If you’re dealing with a PDF file that mostly consists of text you will get much better results using the text comparison option, but the appearance option will also help highlight differences when documents include images.
I haven’t used DiffPDF as much as WinMerge or DiffMerge, but that is expected since it’s not often that I want to compare two PDF files. It is free though, and I’m sure it will be helpful for some people.
DiffPDF Homepage (Windows only; Freeware)