It's been a while, but if I remember right PDF is nothing more than PostScript with extensions by Adobe and a PDF pre-amble. Essentially, it is structured text based on PostScript with the possibility of added embedded binary streams for things such as forms. Given this, implementing a good compare tool should not be too difficult.

The hardest parts would probably be scoping to figure out what Adobe extensions to support, and acquiring or reverse engineering the Adobe extension formats.

Simple PDF example:

%PDF-1.3
%‚„œ”

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<<
/Type /Catalog
/Outlines 2 0 R
/Pages 3 0 R
>>
endobj

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<< /Length 1074 >>
stream
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/F1 0027 Tf
57.3750 722.2800 Td
( A Simple PDF File ) Tj
ET
BT
/F1 0010 Tf
69.2500 688.6080 Td
( This is a small demonstration .pdf file - ) Tj
ET
BT
/F1 0010 Tf
69.2500 664.7040 Td
( just for use in the Virtual Mechanics tutorials. More
text. And more ) Tj
ET
BT
/F1 0010 Tf
69.2500 652.7520 Td
( text. And more text. And more text. And more text. ) Tj
ET
BT
/F1 0010 Tf
69.2500 628.8480 Td
( And more text. And more text. And more text. And more
text. And more ) Tj
ET
BT
/F1 0010 Tf
69.2500 616.8960 Td
( text. And more text. Boring, zzzzz. And more text. And
more text. And ) Tj
ET
BT
/F1 0010 Tf
69.2500 604.9440 Td
( more text. And more text. And more text. And more text.
And more text. ) Tj
ET
BT
/F1 0010 Tf
69.2500 592.9920 Td
( And more text. And more text. ) Tj
ET
BT
/F1 0010 Tf
69.2500 569.0880 Td
( And more text. And more text. And more text. And more
text. And more ) Tj
ET
BT
/F1 0010 Tf
69.2500 557.1360 Td
( text. And more text. And more text. Even more. Continued
on page 2 ...) Tj
ET
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( Simple PDF File 2 ) Tj
ET
BT
/F1 0010 Tf
69.2500 688.6080 Td
( ...continued from page 1. Yet more text. And more text.
And more text. ) Tj
ET
BT
/F1 0010 Tf
69.2500 676.6560 Td
( And more text. And more text. And more text. And more
text. And more ) Tj
ET
BT
/F1 0010 Tf
69.2500 664.7040 Td
( text. Oh, how boring typing this stuff. But not as boring as watching ) Tj
ET
BT
/F1 0010 Tf
69.2500 652.7520 Td
( paint dry. And more text. And more text. And more text.
And more text. ) Tj
ET
BT
/F1 0010 Tf
69.2500 640.8000 Td
( Boring. More, a little more text. The end, and just as
well. ) Tj
ET
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[/PDF /Text]
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/Name /F1
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<<
/Creator (Rave \(http://www.nevrona.com/rave\))
/Producer (Nevrona Designs)
/CreationDate (D:20060301072826)
>>
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trailer
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>>

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%%EOF