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Ezpdf reader is an another product that has annotation features.
Can't you enable annotation using Acrobat Pro on the desktop? In an academic setting it should not be all that hard to get access to the necessary software (by means of academic licensing agreements, or just the computer in the next office...). I'm interested in doing this too (thinking of getting a Nook just so I won't be carrying reams of .pdf's around) and I'd be downloading most of them to the desktop at work, via my university's library's subscription to Science Direct, etc. So it seems like it ought to just be a quick extra step, unless I'm missing something.In theory both ezpdf and repligo should work. But in practice very few pdfs give permission for annotation. So basically they are a rip off.
*bump
My motorola xoom arrived today and I've been taking notes most of this year, annotating lecture slides etc. on iAnnotate on the iPad. I have to say both repligo and ezpdf are pathetic by comparison.