Pigeonhole organizers or boxes with small compartments for different subjects played a large role in storing information since at least the seventeenth century. My thesaurus tells me that it can also stand for a general concept that marks divisions or coordinations in a conceptual system. We all know them as mailboxes (of the physical sort).
There is a piece of software that aims at reproduces this functionality electronically. It's appropriately called Pigeonhole organizer.
It's an interesting idea, but I am not sure I would pay $19.99 for it. There is a free version, limited to just one pigeonhole group, however. And you can try it out to see whether you like it.
Pigeonhole organizer reminds me of another application I tried for some time, namely Notebox Disorganizer. Its concept appealed to me. But in the end, I could never really make it work for me.
Both of them look very much like applications that try to make a spreadsheet-like front end productive for note-taking and writing. Pigeonhole organizer aims more at note-taking, Notebox Disorganizer more at writing. It may well be that the metaphor is "easy to understand and navigate ... that all your notes are spread out in plain sight ... [that] nothing is hidden away in a database or lost in an outline 'tree.'" But the front end gets more in my way than it helps me. I like applications that let you get in medias res right away, like a personal wiki, over which you have a great deal more control.