PdfMasher is a tool to convert PDF files containing text into a ready-for-ebook set of HTML files. Most ebook readers support PDF files natively, but it's often a real pain to read those documents because you can't control the font size of the document and have to resort to the zooming feature instead. Another drawback of PDFs on ebook readers is that annotations are not supported. Unlike other tools that convert PDFs to ebooks, PdfMasher does not try to guess the role of each piece of text in the PDF, and instead asks the user about the role of each piece of text, and does so in an efficient manner.
jbookshelf is an electronic book collection organizer and reader. It supports collecting plain files (text, HTML, PDF, etc.), has basic collection search, fulltext collection search (planned), internal viewers for plain text, HTML, RTF, and PDF, notes and citations, book categories, FB2 support (planned), and portability (removable drives support) (planned).