[ilovejedd]

For fiction, I'm leaning towards something XML-based for a master/source format. The structure lends itself quite well to digital publishing/ebook transformation. epub's a good example of that. Even Microsoft's .LIT is somewhat XML based, albeit, encapsulated in a prioprietary DRM format. I didn't check the numerous implementations but I think for a master file, an XML with a simple layout would be ideal.

<xml>
  <title>some title</title>
  <author>some author</author>
  <cover>some cover.jpg</cover>
  <published>some date</published>
  <description>summary</description>
  <toc>
    <entry>
      <title>Chapter 1</title>
      <description>short chapter summary?</description>
    </entry>
    <entry>
      <title>Chapter 2</title>
      <description>summary/whatever</description>
    </entry>
    <entry>
      <title>Chapter 3</title>
      <description>summary/whatever</description>
    </entry>
  </toc>
  <entry>
    <title>Chapter 1</title>
    <content>Chapter 1 text here (possibly in HTML/XHTML format)</content>
  </entry>
  <entry>
    <title>Chapter 2</title>
    <content>Chapter 2 text here</content>
  </entry>
  <entry>
    <title>Chapter 3</title>
    <content>Chapter 3 text here</content>
  </entry>
</xml>

Another option, instead of embedding chapter content into the file (might make for gigantic XML files for long books)

<content>Chapter 1 text here (possibly in HTML/XML format)</content>
can be changed to
<link rel="alternate" href="chapter1.html" />

Mind you, I'm not very familiar with XML as evidenced above, but the sample layout should give you a general idea. From the XML, it would be fairly trivial to convert to other formats. I think the least formatting available on the master XML, the better since that gives ebook creation/conversion utilities final say in how to handle style, flow, etc.

For reference and technical material, I think TeX is the obvious choice.

Edit:
Oh, whoops. Misunderstood the question. Just goes to show if you can barely keep your eyes open, you have no business replying on forums. To answer your question, given currently available software and utilities, I'd keep ebooks in both ePub and single HTML format. ePub for the metadata, cover, etc. Single HTML files for ease of editing and reading on the computer. As much as I love Calibre for general ebook management, I don't really like its built-in viewer.