I'm putting together the research proposal for my MSc thesis project, so am eyeball-deep in journal articles while reading up on methodology and background theories. I could have killed a small forest to do this - I've built up a stack of 440 papers that are related to different parts of my project. But, I think I may have only printed one article out of that. I'm using Papers to find and manage them all, and it keeps blowing me away how powerful it is at smoothing the process.
Papers is basically iTunes for academic publications. Journal articles, book chapters, etc... It integrates with a bunch of search engines, including Google Scholar, Citeseer, JSTOR, and a bunch of others, to find articles - and download the PDF and metadata for articles. The desktop app is amazingly powerful, and works exactly how I need it to - obviously designed by people who actively search for journal articles. Check out the feature list on the Mekentosj site. Insane.
It also integrates with our campus library's proxy server, so we can access stuff that's licensed by the U of C. Again, insane.
I've created folders (it also supports tagging, but I haven't explored that yet) for a few other topics to help organize the 440 articles into something I can tackle somewhat efficiently. The "background" folder has 40 articles in it now, and I just skimmed them all on the iPhone using the native app - adding star ratings and notes to prioritize and filter articles that aren't relevant to what I need. After syncing back with the desktop app, I have this for background papers:
Still, a bunch to work through, but I'll ignore the 1-star papers. Sorting by descending star ratings, I'll start with the most "relevant" papers. I can also sort by number of citations for each paper, to tackle the most "important" papers first. Very cool stuff. Of the 40 papers, there are 7 that are primarily relevant must-reads. I'll start with those. Then, I'll work through the 7 somewhat-related papers, then the 5 tangentially-related papers, and, if there's time, the 6 barely-related papers. I'll skip the 18 mostly-unrelated papers for now.
I can't wait to scrounge up enough loose coins from the couch cushions to pick up an iPad (sorry, Reverend). That'd be the perfect form factor for crunching all of these articles, and the native app is already there.