PDFs can be read as-is in the majority of e-book readers, including the Kindle. Exporting to PDF is best when you want to maintain absolute fidelity to page layout -- images, typefaces and so on.
Ironically, this is the very feature that can make PDFs a problem in some scenarios, which I hinted at before. Other e-book formats are designed to work independently of any particular device resolution, so pages reflow automatically for each device. This is one of the reasons the Kindle didn't make use of page numbers at first, since the page numbering for a particular book could vary depending on what device or screen size you were reading it with.
PDFs, on the other hand, reproduce as closely as possible the formatting of the original page, no matter what the size of the destination device. A PDF formatted for an 8.5-by-11-in. page may be quite readable on a large display, but looks cramped on a Kindle or Nook. Some PDF readers, such as Adobe's own Acrobat Reader application, are able to reflow a PDF to fit an arbitrary screen size -- but this isn't a universally available function, and you shouldn't count on it being present.
If you're committed to using PDFs, you may want to consider exporting your document with different page sizes as a courtesy for people using e-readers with small screens. This may require some research to figure out what page sizes render best with popular e-book readers.
Elements to include
When you're building a book, elements that you've included in the original document may need a little extra work to translate properly into the finished product. In addition, some elements that didn't seem important for a print publication may be more useful in an e-book.
Tables of contents
An e-book that isn't properly chaptered is difficult to navigate -- doubly so with devices where going to an arbitrary point in a book is not as easy as it should be. The Kindle, for instance, has no touch screen, so jumping around in a book without a table of contents is a chore.
This is most important if you want to set certain elements apart from the rest of the text -- such as examples of code in a monospaced font. This isn't so much a formatting issue as it is a conversion issue, since font choices can sometimes get stripped out entirely during the conversion process, or not be supported at all on some target devices.
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