Let it not be said that I don't respond to readers' comments. A few posts ago, I was moaning about my inability to read journal articles in an efficient and non-fattening way. Yami McMoots requested that I share my system for organizing journal articles, writing that "Curious people who are finally getting quasi-permanent office assignments and file cabinets want to know."
The succint answer: Invest in a copy of EndNote or similar and a thick stack of file folders. As soon after downloading/copying/printing a journal article, add it to your EndNote library. For paper articles, create a manila folder for each 1st author. For PDFs, name them by authors, year, and any other identifying info (subject? journal?) and put them in a folder by letter of the alphabet.
The rationale: I've tried other methods (subject folders, general letter of alphabet folders, by class, by journal (the worst!)) and all have dissapointed me or become too cumbersome. This method takes me a little bit of effort up-front but is much easier to use in the long run.
We've all seen the professors whose offices are overflowing with stacks of papers and books...don't become one of them. Start using a system as soon as possible in grad school, because it will be hell to catch up with the backlogged paper buildup if you don't.
In Endnote, use one of the superfluous headings (I use "notes") to designate whether the article is paper or electronic, if it was assigned for a class, or if it is filed someplace weird.
I started with multiple end-note libraries. One for thesis, one for -ology #1, one for ology #2...and these were keyed to certain drawers in my file cabinent. Lately I've just been adding everything to my thesis library (and drawer), rationalizing that it won't make sense to keep my thesis papers separate once I'm done with my Ph.D. The jury's still out on this one though. I'm starting to think it will make it harder for me to find pure-thesis papers as it get into the final throes of writing.
If you have a lot of papers by a single author, divide them by subject or year, whatever you can clearly label or delineate.
In a few cases, I've lumped a paper with a terminal M.S. students first author into the folder with their advisor's papers. But I always make sure to note it in endnote.
When I'm feeling really overwhelmed and just don't have to deal with new acquisitions, I put them in a designated place until I can get at them. That way I always know what's been endnoted and what still needs to be done. No point hanging on to a PDF or paper if you are never going to recall you have it.
If you have a PDF, you can cut and past the abstract/keywords into endnote. This will make searching your library easier later on. If there are keywords that the authors didn't include, but that I might find helpful for categorizing a paper, I'll add them.
Some journal sites and databases will import references directly into Endnote for you. This is a time saver, but one caveat...think really hard about importing a reference for a paper you don't yet have. I remember how frustrated Writer Chica got during her M.S., because she could never figure out which papers she had and which were only references she had meant to get.
This kind of feels like an ad for a software product, but I honestly can't imagine scholarly life or graduate school without it.