mdepub is a tool that allows you to compose a book in Markdown format and use Pandoc and Calibre to compile an Epub package including all of the book's source material. In effect, you can keep the source and product in the same file in your library; if you ever want to revise the product, you merely need to extract the source, make edits, and recompile.
Bookling is a simple eBook manager designed to make reading fun. It allows you to store, manage, and read your eBook collection on a desktop computer. It features multiple views for your library, multiple bookmarks, customisable fonts and colors for your book's text, and the ability to store your book collection in your choice of directory. Its back end is cleanly separated from the front end, allowing developers to easily port it to other platforms with a native GTK+ or WPF interface.