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The typical methods are: EPUB into kindlegen, Mobipocket Creator, or the Kindle plugin for InDesign. In every case it really comes down to how much time and money the publisher wants to spend making the book look good.
Amazon's format (MOBI) is simpler in nature than EPUB. Some people prefer this because it reduces the amount of variation between books to a degree.
Going off of other people's advice, download the samples for books your interested in from a variety of stores and see which you like better.
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