Create one file in a format that flows the text to fit any sized screen at any level of magnification. This is the approach taken by most ebook formats such as Kindle's.
PDF is not a suitable solution, there are just too many different sized devices.
Publishers can elect to create their own Kindle books in-house by using a free
software program called KindleGen. This is a command line tool that allows you to
build a Kindle book based on HTML, so content in either HTML, XHTML, or IDPF 1.0
or 2.0 (OPF + HTML) is the best source for incorporation into an eBook.
(*from Amazon Kindle Publishing Guidelines)
HTML is also a pretty good format for publishing online ;-)
I note that I can read ebooks downloaded from Project Gutenberg on my Kindle. So It is clear you can publish ebooks for Kindles without being tied to Amazon. I suspect that if you want copy protection on Kindles you may have to go through Amazon and pay a tithe. Of course this sort of (unprotected) content works on any device with a .Mobi reader.
Unencrypted Mobipocket books can be read on the Amazon Kindle natively as well as in Amazon Kindle apps on Mac OS X, the iPhone, Android devices, Windows, and Windows Phone devices. By using third-party programs such as Lexcycle Stanza, calibre or Okular, unencrypted Mobipocket books can also be read on Mac OS X, the iPhone, Android devices and Linux.
Long term plans for the Mobipocket platform are in question in the wake of Amazon's announcement of the Kindle Format 8, which moves in the direction of HTML5 and CSS3.
So HTML + CSS seems a good direction, at least as a common intermediate format.
As an aside, I would start with Plain Text Markup like Pandoc's superset of Markdown and generate other formats using something like PanDoc.