My sister and I have been having a discussion about the best way to organize your electronic files, in particular .pdfs of publications.
I suggested using long filenames (which I learned from my master's thesis advisor). For example, the famous superconductivity article
J. Bardeen, L.N. Cooper, and J.R. Schrieffer, "Theory of Superconductivity," Phys. Rev. 108, 1175-1204 (1957)
could be saved as
SC-bardeen-cooper-schrieffer-theory-of-superconductivity-pr-v108-p1175-1975.pdf
"SC" is a category label for superconductivity. Then you could use UNIX commands like grep to search for the words in the filename.
My sister didn't like that idea, so she asked around and her friend suggested using JabRef. I haven't tried it out, but apparently it's a Java based (thus platform independent) program that can understand LaTeX's BibTeX format. The screenshots look pretty good. You can search by author, title, etc. and see the abstracts in a subpanel below the listings of your collected publications.
If you're paranoid like me and worry about depending on any software more advanced than emacs, you could implement both systems!
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