Most of that non-free software is trash from what I have experienced. Need examples. PDF2HTML is freeware and works decent in complex mode, but when you do this, it generates a full page background image, which will not convert to .mobi format. However pages are preserved 1:1 (but text will not reflow) When you use simple mode formatting is garbled.
There are a few online converter programs but they limit the filesize to 2mb or something stupid, or want you to pay. Most do a decent job, but online uploads of large PDFs is not really acceptable.
Acrobat 9 extended is the best I have seen so far (converting to .doc, .rtf, .html all yields similar documents)
Another option is using Open Office with the free PDF import plugin. You can then EXPORT with various results. It seems to want to export as a slideshow, but people have said they can get it to reflow text and such.
I have had no such luck working with it.
Of course all of this could be fixed, provided amazon updated their PDF reader gui/software.
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