I'm bad with it, journal articles everywhere and I have a tendency to print chapters/papers several times in order to annotate them.

I can't read off the screen. I always miss stuff. Not to mention I tend(ed) to grab papers and read them/scribble on them for an hour before bed quite frequently.

I do feel a bit guilty when I see all that paper sometimes though. Then I just shove it under the bed, innit.

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If you are doing a PhD that doesn't have its articles in journal form but instead you have to photocopy books, etc, then you might want to check if your library photocopy machine can "photocopy to PDF". This then creates PDFs that have images in them. You can then use Qiqqa (pronounced "quicker" and available at www.qiqqa.com) to organise these PDFs with tags and annotations. The best part is that Qiqqa will run OCR (optical character recognition) on your PDFs so that you are able to search the full text for information (be sure to look for the "approximate search" settings in the search box.

Using software like Qiqqa means you won't end up with a digs room looking like a recycling plant with all your annotations buried somewhere inside. :-)