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I have tried tons of options and I currently read and annotate almost everything on an ipad (tenure-track assistant professor in Finance at a research university). I said almost, because I also use a MS Surface Pro. It's too heavy to hold, but, when you use it while sitting at a desk, it's a much better annotating experience than any iPad.
Regarding software - I like GoodReader, but I am not up to par with the most recent updates. When I originally compared them, I preferred iAnnotate - and I stuck with it. I looked at GoodReader once or twice since - and both packages had added features. Yet, I couldn't see a reason to switch. I wonder if anyone has compared the two recently, I would love to hear a detailed comparison.
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