One of my favorite thing about ebooks is that I can make as many annotations as I like. While I do mark up pbooks (not library or borrowed books... just the ones that I own), these mark ups are generally limited to underlining. The margins are not big enough for much else.
I prefer books that stand up to multiple readings: first reading is for content, subsequent readings are for enjoyment and edification (or more precisely, enjoyment through edification). I try to make note of any similarities that I see to other books, or my life, or world events, or whatever. I like looking back at my earlier responses to a text and seeing if I still feel the same way the second, third, fourth time that I read it. I also make predictions regarding what will happen next, and I like being able to quickly refer back to whatever bit of foreshadowing that I spotted (or that I spotted in hindsight on a subsequent reading). If I jumped on to wikipedia to double check something, I usually make a quick note of it. For instance, I'm reading Anna Karenina at the moment, and went to wikipedia to get a quick overview of Tolstoy's views on communism.
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