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Use FileMerge to diff PDF files
Not wanting to sound like an old fogey or anything, but FileMerge cannot hold a candle to Emacs' Ediff compare tool. Start any version of Emacs (but Aquamacs is great with MacOS/X), and select Tools->Ediff->Compare up to 3 buffers or files. Ediff highlights word-for-word differences rather than whole paragraphs and is much much better than FileMerge at ignoring whitespace differences and finding the places in the 2 or 3 buffers that do match up. type 'n' or 'p' to move forth and back between differences, and 'a' or 'b' (or 'c') to select the correct version in the output.
It is less pretty than FileMerge but much more effective.
Use FileMerge to diff PDF files - also for PDF?
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