I'll be the one to say the Calibre is a phenomenal piece of work. Its ability to scrape hundreds of sites into epubs for my phone, tablets and ereader have been very helpful, especially given that I can tweak the code for a given site to get exactly what I want. I have it set up to mail my Nook Color the news every morning so I have it to read on the train on the way to work. Its ability to fire up a content server and serve up all my books eliminates my need to ever manually sync any of my readers that support fbreader on Android. It has excellent metadata editing features, and immediately made my Gutenberg collection much more attractive by going to out the web and collecting covers and metadata for them. It is very actively maintained, and has supported every reader I've thrown at it: my old Sony Pocket Reader, the new Simple Nook, the original Nook, a rooted Nook Color, the Nexus One and an Asus Tablet.

Given that it calls lots of helper utilities to do conversion between formats, it would be easy for someone that had a problem with the conversion utilities to write new ones and have those used instead.

As for Qt dependencies, Calibre is one of the few programs I don't pull from package management, since it is updated far too frequently. Instead, I have a cron job that checks for and installs new versions twice a week, and the executables live in /opt.