I just saw the program for the TeX User Group (TUG) conference this year:
http://tug.org/tug2009/program.html
Two talks struck my eye:
Ross Moore: "Towards tagged PDF"
Kaveh Bazargan: "TeX as an ebook reader"
The first suggests that they're working to make it so that pdfLaTeX handles inserting tags, for properly reflow-able, cut-and-paste-able PDF output from TeX source.
The second suggests that packages, or perhaps even new output profiles, are being worked on for .tex source to create ebooks... (A TeX>ePub profile even?) ... although it's hard to tell from the title.
Either would be a huge step forward, but makes me wonder if in fact, PDF does still have a place as an ebook format for the future. It also makes me wonder if anyone will be using BookDesigner or similar software if the wonderfully powerful resources of TeX become available to ebook creators!