As we try to move towards paperless offices, one of the big challenges is finding the right way to file and organize PDFs of interesting papers, books, reports, proposals and what have you. ScienceSampler suggests using iTunes, and that’s certainly not a bad idea. iTunes acquired the ability to handle PDFs in order to handle liner notes, and you can associate various forms of useful metadata with your PDFs.

My preferred solution, imperfect though it may be, is Yep (née kip), available only for Macs. Yep lets you tag and label your PDFs in various handy ways, and is even designed to integrate with your scanner, so that you can scan in important documents and automatically store them and, more importantly, retrieve them.

I don’t love the whole “tagging” interface that seems so popular on websites and in applications, but I think that being able to organize PDFs into a web of relationships is very useful. In writing a paper, it’s nice to be able to search your PDFs for the the papers that talk about “competition” and “niches” and “voles,” then pull out their citations and move on. I wish there were a better way than tags to do that, but there isn’t, and Yep makes it easy to reuse tags, keeping your usage consistent. It even tries to auto-detect meaningful tags in new documents.

It costs a little money, but I think they’ve earned it. A tool designed to handle PDFs is preferable to one designed to organize music.