This is a question that comes up semi-regularly and a search of HN might yield threads that are interesting to you. On thing that I haven't seen mentioned so f

This is a question that comes up semi-regularly and a search of HN might yield threads that are interesting to you. On thing that I haven't seen mentioned so far is an idea of mine which might be useless but I want to share it anyway: Maybe you should think in bigger terms and not consider a single application (or a set of applications) your knowledge base, but an entire computer set aside for this purpose. The advantage would be superior flexibility when dealing with a large number of different files and file types; plus you can use operating system features such as tagging on Mac OS X.