PDFMasher is a tool to convert PDF files containing text to MOBI or EPUB. 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.
Enter PdfMasher. PdfMasher asks the user about the role of each piece of text, and does it in an efficient manner. Your PDF has a header on each page and you don't want them to litter your text? Sort text elements by Y-position (thus grouping them all together), shift select the elements and flag them as ignored. They will not appear on your final HTML. Your PDF has footnotes on many pages? Sort your elements by text content (thus grouping all elements with the text starting with a number together) and flag them as footnotes. They will be moved to the end of the document, and PdfMasher will try to create hyperlinks to footnote references.
NOTE: Although this software is listed as "Free", it's actually Fairware.