The most flexible and most widely accepted format, as well as being the most advanced, would be HTML5. It is not specifically an e-book format, of course.
Most of the e-book formats simply re-package text marked up in HTML. The concerted promotion of the ePub format for the last 5 years probably makes it the single-file format most widely included among an e-reading system's options. EPub files without DRM are simply zip archives whose extensions are .epub instead of .zip, so they are easily dismantled and edited.
There are many disadvantages to the PDF format but it is not limited in terms of quality or availability on various platforms, and there are many commercial and free applications for editing and/or creating PDF files.