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Calibre is free (they ask for a donation, which I'm going to give them soon), but it is a Universal format <--> format converter, which has a nice Windows interface, and is quite intuitive.
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I use calibre quite a bit myself for personal things. I'm a huge fan. I think it does a fantastic job of translating css-laden ePubs into comparable MOBIs (often times better than kindlegen). However the MOBI format is still proprietary and owned by Amazon. And no matter how thoroughly reverse-engineered the MOBI format seems to be (by calibre developers and others), the anal-retentive, compulsive, perfectionist in me isn't willing to take the chance (when uploading to Amazon) that something will be missed, or that something will change. So when uploading MOBIs to Amazon, I stick to the official Amazon tools for creating MOBIs. Not out of loyalty, but out of paranoia that something else may not get every tiny, internal detail "right."
Often times, I'll use calibre to get a MOBI that looks the way I want it to, then unpack that calibre MOBI and rebuild it with kindlegen, just to be on the safe side.