When it comes to eBooks, Marvin for iOS has a great system where you can easily select/highlight entire sentences. If I want to add a note, I choose the highlight and annotate option and then dictate to siri what my note is. That works pretty well, and I can then easily export highlights and annotations to email (and then another system).

For pdf's I use Goodreader, and the same annotation technique.

Still not ideal though. I would be very interested in an app where I can highlight text and immediately dictate (or record) comments without an extra tap...