I was wondering if any academics out there have gone paperless, and how they might manage with the stack of journal articles I'm sure most of the rest of us have piled on their desk.

My reasons for wanting to go paperless are rather obvious: I just have incredibly tall stacks of papers that I can't cross-reference very effectively, and filing is a nightmare (I could probably fill an entire drawer in under 6 months). Not to mention that I can never find what I'm looking for when it becomes critical. I've been using Papers (by mekentosj) to archive and organize my articles, and that has been working out pretty well (although I hope they add some robust tagging support soon).

So my main question for those of you out there is how you keep track of any note-taking you do on papers? What I'd really like is an effective way to highlight - make text annotations - draw pretty arrows/circles - curse out my competitors - you know, smart people stuff. Ideally I could do this while reading it on screen, but there's also something romantic about pen and paper (my GTD system is analog) - so I may just annotate the pdf after the fact.

Does anyone do this regularly as part of their workflow? Could you recommend a good tool for all these annotations (for os x)? Or worst case scenario - do you have a really great filing system for academic papers? Just about everyone I know uses the stack-it-until-it-falls-over method.

Cheers.