@nickredding: The difference between windows and kindlegen is that while the user *already* has windows, she may not already have kindlegen. In other words, calibre does not distribute an operating system of any kind open or closed source. When a user downloads calibre they are guaranteed that every part of calibre *itself* is open source. That little fact allows me, for instance, to make claims like this:
http://manual.calibre-ebook.com/faq....a-virus-trojan. You may well be comfortable with using binary blobs for your software, not everyone else is, and I suggest you not dismiss their concerns out of hand. It is for this very reason that I refused to include the opencandy binary blob into the calibre installer, despite the fact that it might have increased my income from calibre.
To me one of the coolest things about calibre is how quickly bugs in the conversion engine are fixed, when they can be fixed. Relying on kindlegen means I would be forcibly reduced to depending on Amazon, and given the utter lack of quality in their ebook software division (something you as someone who has worked on MOBI can attest to) that is no small thing.
Finally, my main motivation in writing calibre is to prevent the ebook ecosystem from relying on corporate entities and closed source software. In other words, one of my goals is to make knowledge of ebook formats available in the public domain. To me, reading and ebooks are important enough for that to be essential.