I like to use the file system. And I like to use the file system's default explorer: On the Mac this is the Finder, on Windows this is the Windows Explorer, and on Gnome it is/was Nautilus. I much prefer to have other tools integrate into the file system explorer than for the tool to have its own explorer.
When this happens, it is then possible to create your own tools that support your workflows. (Note that in this posting I am concerned with explorer integration and not command line integration.)
Unfortunately, this has not been the norm and so we have iPhoto, iTunes, etc, having there own content organization that is independent of the file system. These content specific explorers are often created due to the weaknesses in extending the system's explorer but mostly it is because creating another explorer is just easier to both imagine and code. The up-shot is that we have organizational silos with little integration between them. And, worse, the inability to create your own specialized tools from the integrations.
This Sunday I spent far too much time tracking down tools that would allow me to use the file system to collect and organize content as follows:
1. Each content collection is a folder. I am comfortable with using the file system hierarchy for organizing and I am aware of the weaknesses of hierarchical organization. However, most collections can be organized into a primary hierarchy and augmented either by search or linking (aliases on the Mac and shortcuts on Windows).
2. Each folder will have, at least, one plain text file of dated notes. Each note is separated by a simple delimiter, for example, a row of dashes. My experience is that this one file of notes is much easier to review and keep updated than to place notes into individual files. With that said, a good tool that can hide the file-ness of the notes would be acceptable too. Until then, one file of notes and using Merlin Man's tip for adding content to it <http://bit.ly/a1kfV6> will do fine.
3. The primary hierarchy needs to be supplemented with full text search. Tagging is not enough and, moreover, tagging can be achieved via search by using specialized tokens: For example, in normal English typography a colon is always followed by a space and so the expression ":foo" distinguishes the tag "foo" from the rest of the text. Spotlight on the Mac is the system's full text searching facility. It is extendable so that other content types can be incorporated. The plugin I am looking for would index the dated notes in a file as collection of "records". (This Spotlight feature was introduced in OS X 10.6.) The Spotlight plugin is the most specific tool that I need. While it is a Mac only indexing solution it is based on plain text content and so could be indexed easily under other operating systems. Unfortunately, as far as I can tell, and I spent a good amount of time looking, there is no plugin for indexing delimited content as records. There are plugins for content types that somewhat match, for example mailboxes, but there is no documentation on how to use them outside of their intended application. The up-shot that that for this very simple workflow I can not compose a supporting tool from existing parts. Looks like I am going to have to write my own Spotlight plugin: If anyone has skeleton code I can build upon please drop me a note.