For Mac there is this nice shiny aplication called skim, that looks very nice. You can add notes, highlight (two-column does not work) and export the notes. The notes appear as a list in a sidebar as you work. Importantly skim stores the annotations in the file itself. So why am I not using smim yet? Unfortunately the annotations seem to be in a skim specific format, so that preview can not pick it up (and so acrobat reader might not either). Skim is not available for windows, so I'm not sure if I should lock myself in.
gattach was a handy tool to use for webmail clients like gmail. I couldn't find it anymore, but then from this discussion I found out that gattach is now affixa.
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