One thing that wasn't clear before... at least, not clear to me... is that the new KindleGen is a command line program intended for the batch-processing of many books at once.
In other words, it is intended for large publishers.
Small publishers and authors are still advised to use DTP (which this forum supports).
As far as I can see, there is only one reason for a small publisher or author to use KindleGen... If you do not use Windows, you need something other than Mobipocket Creator.
Below is where you will find the new 72 page manual "Amazon Kindle Publishing Guidelines", and you can also download the new KindleGen (if you need it)
Amazon Kindle Publishing Tools
I don't represent Amazon, I'm just posting the below for the benefit of those who have not been able to find this information... it's copied directly from the Amazon page.
• Small publishers and authors can take advantage of Amazon's self-service tools through the
Digital Text Platform (DTP).
• Publishers who have a relationship with an Amazon Kindle vendor manager should read more about Kindle Title Manager.
• Publishers and individuals who are comfortable working with HTML can use KindleGen (see the KindleGen section below) to create content, and eBookbase to upload files.
KindleGen is a command line
KindleGen for Windows (2003, XP, Vista, 7)
KindleGen for Linux 2.4 i386
KindleGen for Linux 2.6 i386