With Kindle personal documents, there is copy to clipboard. Then from there you can paste to another app.
A number of apps, like iBooks (but not Kindle, which only does FB/TWTR/GR sharing and copy/paste), will let you share highlights with other apps, such as Evernote, OneNote, etc. So as long as you do that as you go along, you can keep a notebook of everything. That is the best solution I've arrived at so far.
Gerty (same developer as Marvin, iPad only I think) has a 'Reading Journal' that captures all of your notes from everything you are reading with it, including time and location tags. These can be exported to an ePub file. Then you can share that (Mail, Dropbox etc.) or Open In. But curiously it doesn't seem to let you highlight anything. It also has scrolling mode, which obviates the need to highlight 'across pages'. Interesting app, but I'd like more 'atomic' sharing with Evernote etc.
Finally there is a brute force method that will work with any app: screen capture. Then you can go to Camera Roll and share with another app, including for example, an OCR app that will turn it into text that you can in turn copy or share with another program. I think Evernote will look for text or handwriting in image captures and allow search by that text (though it is not OCR as such).
Mantano Reader is interesting as well, and does well up to a point. But there are no sharing options, and all you have is cut/paste. Not sure how you get them out of the reading app.
It is really weird that there don't seem to be many apps that let you export all highlights/notes in some convenient fashion.
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