During a recent meeting, we discussed ways to corral the billions of pieces of loose paper (hello, journal articles!) that will be infesting your living room, bedroom, bathroom, kitchen...
Aya highly recommends Zotero, a free download from Firefox that works like Refworks and EndNote, only better. She also uses super-teeny post-it notes that are common in Japan (and you can find them at Huntley Bookstore). The smaller size gives you more room in the book / on the page for flags - and helps you keep your own note-taking down to the bare essentials.
Margaret swears by her system of color-coded index cards with corresponding colored file folders. For example, one folder says "Chapter 1" and what will be in that chapter. When she reads something she thinks should go in Chapter 1, she tapes it to or prints it on that colored paper and files it away for later. This is great for tidbits you don't need now, but you'll want for later. She has also created an Excel chart for all of her literature.
In terms of creating multiple labels for your binders and files, Bennett recommends his trusy Brother Label Maker.
Finally, for extra help getting through the massive organization needed during the literature gathering process, you might consider hiring someone for assistance. You can easily advertise on campus, through the CGU student listserv, or in a local paper like The Claremont Courier. Hiring extra help can be a mutually beneficial experience - many new graduate students would appreciate the hands-on experience of working with a dissertation.
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