You don't need large margins to write your notes in (and I don't think you will find a lot of ebooks with very large margins). In the sony touch you can highlight a word or passage and then add your handwritten or typed notes in a pop up window. I never took notes on paper books, but I use the feature all the time now.
Of course you can also write or draw directly on the page too, and choose to not display notes when you feel they get in the way.
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