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...

It's not at all well developed yet.

I've been using the Amazon web reader (mostly because I'm in Beijing at the moment and getting anything onto my kindle is a pain). I have the reader full-screen and Atom in Zen mode, and switch back and forth with i3.

For the books already there I took notes as I read. For the current book I'm trying out reading a chapter, writing down notes from memory and then skimming the chapter again to see if I missed anything.

For stuff I want to follow up I've been just putting TODO in the notes rather than breaking the flow.