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calibre-ebook.com]
Open source, freeware, (mostly) intuitive, and can do absolutely anything you need to every ebook format ever (except Word).
[
www.mobileread.com] integrates with calibre and does Word files if you really need to make it appear on your kindle just so. otherwise just mail to to amazon.)
Has a neat RSS feature to fetch then convert news sites and blogs (pretty sure you have to pay for that through the amazon store).
Can also remove the line breaks (even hyphens) in any file (except Word). I bought a 10 dollar (top shelf) book from the amazon store and had to reformat it. Not happy. With this you can look at the file as it would look on the kindle and make it pretty.
Anyway once you get calibre you can go to the less reputable places on the intertubz and get whatever you need (it's fun to get nook files so you can fuck amazon and barnes and noble AT THE SAME TIME).
And, my favorite, you can mess around with your menu, and change absolutely everything (yes, except Word) about the metadata. Title, author, cover page, some other stuff.
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www.mobileread.com] is a plugin for calibre that will let you manipulate the kindle menu, collections, font and margins (pretty much all you can do to the kindle without jailbreaking it) in a GUI. So much easier than making collections on the kindle, especially if you have a shit-ton of books.
After you do all that you just click a button and it updates your kindle (or nook or whatever sony has, apple iOS (reading on a backlit screen is stupid, but whatever)), etc.
Seems complicated, but the actual converter/metadata interface is simple, for the price. Read the manual for the other stuff.
I'll see you next time.