Articulating the ineffable. Programming language theory 
cognitive psychology. PhD @Stanford
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Academic peeps: I may have finally given up and accepted that I may need software to organize papers. Zotero seems the way to go (non-profit)—don't want to shave THAT yak myself. Things to look out for before I start the transition? (Do y'all use Zotero? Use anything else?)
I use Zotero, basically for two things: a) automatic fetching publication metadata for PDF, and b) non-hierarchical organization of papers (vs. using file-system folders). I haven't figured out a good workflow for associating notes w/ papers though.
Sigh. That was going to be my next question. But at least it has tags, so if I need to find "that paper I once read about transfer", I would have a shot…
For associating notes, ZotFile is a free extension that will import any annotations made to the article PDF as notes in Zotero. Highlighted text and notes can then be exported for multiple documents/folders at once into a report
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