PdfMasher is a tool to convert PDF articles (newspaper, academic) to MOBI or EPUB documents. Most ebook readers support PDF files natively, but it's often a real pain to read those documents because we don't have font size control over the document like we have with native ebooks. In many cases, we have to use the zooming feature and it's just a pain. Another drawback of PDFs on ebook readers is that annotations are not supported.

There are already tools to convert PDFs to ebooks like Calibre, but what they do is that they try to guess the role of each piece of text in the PDF (and that's if you're lucky). I think that in all but the simplest cases, it's a mistake to think that anything short of an AI can do that kind of guessing.

http://www.hardcoded.net/pdfmasher/