I'm curious whether any e-reader supports in-PDF annotations. I've done a bit of developing with Adobe's PDF SDK in the past, and found that they were very protective of the features that separate their cash-cow, Acrobat, from the free viewer programs. Annotations fell squarely into the for-cash features of PDF. I suspect that any program that supports annotations would not be cheap, and you could expect the cost to be added to the price of the e-reader if available.
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