There are two irritations when it comes to the Kindle. First of those is your collection of PDFs you bought or own that you’d like to read as a ‘book’ on the Kindle (without going through the whole long USER@[free.]kindle.com) email and Whispernet delivery process. The other is the EPUB Sony Book reader format files that you have — but that the Kindle doesn’t interpret. Here’s how to get around this.
PDFs and your Kindle
Possibly the best application on your machine to manage clean conversion of most PDFs (except in extreme cases or file lock etc) is MobiPocket Creator which will do the extraction of text, conversion to .mobi format etc for you. In post-editing, you can add the cover-image, create a Table of Contents (TOC) and add relevant metadata such as author, year, genre etc that will make your referencing your books easier in future. MobiPocket is free and highly capable, though only available for the Windows platform.
EPUB
Now there is an option of installing an application on your Kindle (called Savory) that will open and convert EPUB files on your Kindle – but that means installing a third party application. This is where Calibre comes to the rescue (and I’m sure you have it already). Calibre allows you to do bulk directory conversion, or just per-file conversion from EPUB Sony Reader format to a Kindle-friendly .mobi format (which will maintain element such as cover images, TOCs etc). A 26MB download or so later, the application is quite capable and has already reached version 0.7.20 after extensive development work, and is available for Windows, Linux and the Mac.
Books, Books, Books
Next to the Amazon Kindle store, and Barnes and Noble etc, there’s the Gutenberg project, FeedBooks and ManyBooks that carry a collection of Public Domain books. The benefit is that they are out of Copyright (check in your jurisdiction) and thus available to you to download. And then again, Books.Google.com also makes a selection of books available to download via EPUB format — already since Sept 2009 – but you knew that already!
Remember – do can do all conversion and download on your local machine, and just drag the appropriate .mobi or .azw file to the /documents folder on the Kindle via USB – no need to switch on 3G / WiFi on your Kindle for data transfer!