I ponied up the money and bought Papers recently — it’s not perfect but it does let me store all of those pesky PDFs I have lying around in a convenient single location.
The program acts like “iTunes for your papers.” It has its own internal storage system (which is also customizable) and lets you create collections (e.g. playlists). The best feature is the interface to various repositories such as PubMed, ArXiV, JSTOR, ACM, and Web of Science. It technically lets you search IEEEXplore as well, but IEEE just upgraded their system (color me unimpressed), which broke the current version of Papers’ search interface. I’m sure it will get fixed soon enough.
What I wish it let you do was to tag papers so that you can click on a tag to see all papers tagged with that topic; while this functionality is there, it’s not transparent to do it. I’d also like it if the BibTeX was associated as metadata with the paper file, so that I could integrate it better with BibDesk. I had contemplated getting DEVONthink to organize all of my files, but I felt like that was overkill.
Does anyone else out there have a killer system for organizing papers? I know it’s just a crazy dream that I’ll actually get a chance to read most of the papers I have sitting on my hard drive, but I’ll be more likely to read ‘em if I can find ‘em.