I think your best approach would be to convert the PDF to images at a decent resolution and than do an image compare.
To generate images from PDF you can use Adobe PDF Library or the solution suggested at http://stackoverflow.com/questions/75500/best-way-to-convert-pdf-files-to-tiff-files.
To compare the generated TIFF files I found GNU tiffcmp (for windows part of GnuWin32 tiff) and tiffinfo did a good job. Use tiffcmp -l and count the number of lines of output to find any differences. If you are happy to have a small amount of content change (e.g. anti-aliasing differences) then use tiffinfo to count the total number of pixels and you can then generate a percentage difference value.
By the way for anyone doing simple PDF comparison where the structure hasn't changed it is possible to use command line diff and ignore certain patterns, e.g. with GNU diff 2.7:
diff --brief -I xap: -I xapMM: -I /CreationDate -I /BaseFont -I /ID --binary --text
This still has the problem that it doesn't always catch changes in generated font names.