I'm sure there are some full blown document management solution available, but at a cost. These systems are usually expensive and can lock you in to proprietary file formats, and you may have to pay an annual maintainance charge. Although PDFs are proprietary, the reader is free and nearly all the suppliers use it.

As file systems are currently all hierarchical (until Microsoft next-gen comes along), you can only use one primary categorisation. I use manufacturer because I don't have to think about that too hard. If I'm looking for a chip of a certain function I resort to a table in Excel. I can include a link to the datasheet in an Excel cell so that I can get the datasheet quickly.