Absolutely the #1 use for me is free magazines and newspapers, automatically delivered wirelessly to my Kindle, thanks to Calibre's scheduling and Amazon's free.kindle.com e-mailing. It's the main reason I have a Kindle (also for wireless "Send to my Kindle" bookmarklet clipping), and it's the reason I just added a Kindle Fire (because I want to peruse the magazines/newspapers more quickly). Who doesn't like no-effort free content?
#2: format conversions: mobi to epub, and specifying added fonts via CSS for non-PRS+ ereaders.
#3 (tie): book searching (Get books); reading on a tiny 5" PC (View).
Library organization is almost an afterthought, as I know the original location of my books on my PC (and of course don't need to know the locations of purchased Kindle books). Calibre nicely deletes old newspapers/magazines (you set the interval), but keeps all my ebooks I've imported.
Love it!
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