Book Designer will also work for text-based PDFs. Then save as html. But it balks at image-based PDFS.
I tend to use Mobipocket Creator, which generally works rather well for text-based PDFs. After you load the file it makes an html version and stores it in "my publications."
For image-based PDFs I've invested in ABBYY Finereader 10. It's not cheap but does the job better than the competition, in my opinion.
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