Hmm...referencing line, act, chapter and so forth does not work for the majority of academic texts because we don't sequence our text that way. It's not a play after all. I have wondered about this problem of citation for ebooks too.
Look at this website for a short example of what APA and MLA suggests:
http://www.lambuth.edu/academics/lib...ingebooks.html
However, this is not too helpful because we won't be able to quickly locate a particular quote (no page number cited) unless we use the ebook which then means we'd have to have access to a reader that can read that ebook.