What is the best way to organize items listed above? Are there any tools similar to google notepad or scarpbook firefox add-in? It should allow saving web pages cuts with images, possibly directly from browser, and other documents, especially pdfs and adding notes/tags to their fragments. What do you recommend?
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You may want to check out this link for PDF annotation:
http://en.wikipedia.org/wiki/Comparison_of_notetaking_software
I don't think the following annotate PDFs but they are the popular options after Google Notebook.
I've known people to use Evernote.
If you want to pay there's MS Onenote.
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Evernote would be great if not for lack of pdf annotations. But, on the other side, with 40MB/month free upload, it may be better to keep pdf on different server, and upload to evernote html notes with fragments and links to those pdfs. I will try, if I don't find the ideal tool soon ;)
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