Well, I've belated just discovered Papers (Mac OSX only, I'm afraid), a sort of iTunes for your PDFs. It has been around for over two years -- there's an old explanatory poster here -- and it knocks spots off the various previous solutions I've tried. Here are some high points:
- You fire up Papers and there in its designated folder is your library of PDFs, neatly listed and sorted. Papers uses the Spotlight engine to do very fast searches. You can then click on items to read them from within Papers (and you can write notes too). And you can open different papers in different tabs, rather than have a clutter of windows.
- That's very pretty, but Papers really comes into its own when e.g. you want to search and download papers e.g. from Jstor. You can search Jstor from within Papers (early releases of the program only knew about science databases: being able to work with a wider set of sources is the big new feature added in later versions). You can just store the found paper details for later: but click on the found title you want to fetch, and you get to the paper's Jstor download page. Download the paper, and it arrives in your library, with the author/title/year/journal etc. metadata all neatly listed -- and Papers systematically changes the title of the PDF file itself, from Jstor's to your preferred naming system. (I use author, date, first five words of title). So looking in the library folder itself from the Finder, you see a neatly and usefully named set of files.
- How to you move some previously obtained paper into the library? Or a paper newly downloaded from a current journal issue? No problem, drop the paper onto the Papers icon in the dock, and it will appear in the Library. If it is recent with a DOI identifier, again Papers extracts the metadata and renames the file according to your system. Otherwise you give Papers e.g. the author name and a word or two from the title, and Papers asks Google scholar to find a match: click on the match, and -- whoosh! -- the paper is neatly filed and renamed again.
- With a library full of papers you can then sort them in various ways, and make various "collections" (smart ones too, if you want). As I said, you can of course search your library from within Papers. And because the PDF library remains just that (i.e. the files aren't messed about with) you can inspect it from e.g. DevonThink if you want to do some much fancier "intelligent" searches.
- The thing is a joy to use, as I'm discovering. You can of course export BibTex and other citation data if you want. And the interface is really neat. It was won an award for being quintessentially Mac -- which it is, to the point that they don't bother to provide a manual apart from a short getting-started video. Just remember to control-click on any likely-looking button or sidebar item, and you'll get a drop down menu of options.
- And oh, if you really want, you can sync a collection of your papers to Papers for the iPhone or iPod Touch, to read some PDFs on the move.