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I am not sure what exactly you have in mind - everyone has their own method, I think. I like handwritten notes on my documents - and I don't really tag them or export them. Yet, I think the SONY PRS900, which I am currently using, could do what you ask - albeit not as seamlessly as we might want it to.
For example, you can highlight sections or scribble on the document, then add a note to that with the virtual keyboard (a tag, I guess), then export the whole thing to an RTF. That would get you searchable tags. Then, if you want to organize the whole thing, link the RTFs to OneNote and you have a searchable database of annotations.
As I mentioned, personally I am happy with annotating pages. When I am working on a topic I read papers, annotate them, but then I use the annotated file to write my own lit review. Nothing beats your own summary of a topic. And I don't find extracted snippets all that useful - if I am summarizing a paper, I need the whole paper in front of me. But, as I said, everyone has their own methods.
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