Apple uses standard ePub -- except that it may add DRM for purchased books; its iBook Author tool may use extensions unrecognized by other readers; Apple-specific tools for iBooks: Pages, iBooks Author
Kindle and ePub?"Kindle platform does not support the international ePub ebook standard. However, there is software available (e.g. Calibre) which can convert a non-DRM ePub file into the unprotected Mobipocket format that the Kindle can read. Additionally, Amazon offers a free program called KindleGen which converts ePub and several other formats."
destination issues: fixed layout & page-size on smaller screens
"app" (book embedded): flexibility vs. "standard" navigation (possibly different from eReader apps); less portable across models/devices/versions: developer/author may need to rewrite/retest
Microsoft Word (.doc, .docx, .rtf): public format (but controlled by Microsoft); source: for ePub conversion; destination issues: file, user interface (& maybe font) incompatibilities across Word versions/installations; app large, complex & expensive, though free alternatives are available (Open Office, LibreOffice, Google Docs, ...); user ability to modify the "book" could be disadvantage