My system keeps changing, but at the moment...

Folders - I maintain very broad categories of folder, which are really
only used for the drop box panel. They correspond to the answer to the
question "why am I storing this?" Is it for future reference, research
material to be examined later, a random thought I've had myself, or an
asset that I am trying to create for use elsewhere (e.g. a piece of
documentation)? Sometimes if I'm doing an awful lot of dragging and
dropping from Safari I'll set up a temporary folder for a project, but
I'll tag the contents and delete the folder afterwards.

Tags - most of the classification is done with tags. Material for an
individual project is defined by a combination of one or more tags,
and for all of the current ones, there's a tag folder, prefixed by "."
so that they all go to the top of the list. I used to file projects in
folders, but when you delete a folder you can never find out what was
in it again, and I can never tell when I might need to look at an old
project once more.

(I find it useful to maintain a list of the tags that get applied to
individual projects - I've been experimenting with prefixing all
"project code" tags with "p.", but it's not proved worth it yet.)

Oh, there are also tag folders for "todo" and "idea", though I do most
of my task management with Todoist or Taskpaper. "todo" tagged items
are usually reference data which won't fit anywhere else.

Flags - a flagged item is just one I can get to with the "Flagged
Items" list. It doesn't mean anything more than "I use this a lot" or
"I should pay attention to this" - if I findmyself looking for that
item a lot, I'll flag it, if I find I'm not, I'll remove the flag.

Labels - I don't really use these a lot except as decoration. There
may be a good way to use them - they've got the advantage of being
very visually distinctive - but if there is one I don't know what it
is. Also, they're a bit hard to export if it ever comes down to that.

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