The first e-book format I ever used was Microsoft's proprietary .lit -- which the company has decided to stop supporting. I liked it and it was a rather good format -- the Kindle and EPUB have really only caught up to it recently. Indeed, I don't know if any of them yet have the clean and clear readability of the MS Reader's rendering. But it never gained the popularity it probably deserved, perhaps because it was so closely tied to MS (and to their Tablet PC offerings).
I am leery of proprietary formats in general, so I'm not a fan of Amazon's Kindle offering (while recognizing it has its strengths). Well, I'm not a fan of Amazon anyway. EPUB and/or PDF is the way to go in my, uh, e-book.
If one is reading a book on ones computer, I think PDF is still an excellent choice, especially if the formatting (including illustrations) is an integral part of the product. The PDF is not always the best for portable readers, however, as it may not fit well on the screen. For a novel with a relatively narrow page layout, the whole 'reflowable text' thing may be less of a concern.
I did update to a dedicated PDF e-book version of "The Middle of Nowhere" to make the file smaller and more e-reader and web-friendly. That's at http://www.lulu.com/spotlight/arachispress, of course. In time, there may also be an EPUB copy available but that remains a back burner project for the moment.