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I use Evernote, simply because it was easy to find and free, and I started out using it on my MacBook. But I just set up my Nook Color as an Android Tablet (SD card method) and I downloaded Evernote from the Android market, logged, in synced, and in less than a minute, all my notes were there.
However, these notes were not, of course, highlighted from a book or paper, but I have taken stuff from websites, and any documents I have (copy and paste). I don't know that this will really suit your needs, but it might be something to investigate, anyway.
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After playing around with different readers I switched to mantano reader. I like the fact that changes you make in both repligo reader and ezpdf reader are actually stored in the pdf, so changes you make can also be synchronized to my computer through dropbox, but their reading experience isn't very good on an e-ink reader due to all the page flip animations. Mantano is more easy on the eyes in that regard. Notes can only be synced through ADE, which is a pity, but I'll stick to this reader because it makes the reading and note-taking relatively painless, which is the most important part for me. But thanks for the suggestions!