Compare PDFs with DiffPDF in Ubuntu Linux, Debian, Fedora and Other Derivatives

It looks like pure magic. Older versions was released under GPL2 (though the copyright notice contains "All rights reserved" too, tough call), but newer versions are under a restrictive license.

I wonder how well it works for equations.

http://www.qtrac.eu/diffpdf-foss.html

Note that if you are working on a latex document you can use latexdiff.