ePub. Definitely ePub (but really, why not both?). I have a million PDFs but for reading a book, ePub on either a Kindle or iPad is much more pleasant. I can read a PDF on the iPad or Kindle. But nothing beats reading something properly rendered for ePub: read, read, read, swipe left.

That said, for long ass manuals (the 5,062 page Intel® 64 and IA-32 Architectures Software Developer’s Manual comes to mind) then PDF. Also for published papers. But for books, ePub.

For example, the Pro Git book is available in ePub, PDF and mobi. It is regularly updated.

https://git-scm.com/book/en/v2