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Over the years, I have never, ever written in a book that I was reading. Way back when I was in school, I simply wrote notes in a spiral notebook. More recently, I had note cards and wrote the notes with a book and page notation.
These days, many e-readers allow you to anoint and copy those notes up to your computer. For example, with Kindle on the iPad you can highlight a passage and create an associated note, or bookmark a page. You can then access the annotations via your browser and cut and paste to which ever program you wish. On my mac, I use Yojimbo to hold various bits of info like that. On a windows device I use OneNote (I have an older copy that doesn't upload to the cloud). You could also use evernote.
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