E-Book Library Manager
http://calibre-ebook.com/


E-Book Editor
https://code.google.com/p/sigil/


Fan Fiction Down Loader
http://www.mobileread.com/forums/showthread.php?t=163261


Cover Generator
http://www.mobileread.com/forums/showthread.php?t=124219


Mobile Reads is a great website with tons of help for Calibre!
http://www.mobileread.com/
http://www.mobileread.com/forums/forumdisplay.php?f=166


Academic Paper Organizers
http://www.mendeley.com/
http://www.qiqqa.com/Download