My process has gone through some revisions.  My current setup is as follows:

client-projects.org
I keep all paid projects for clients in one big file.  I used to keep them
in a file for each client until one of them noticed that their name was
being pushed to github in my agenda files.

studio-projects.org
This file holds all internal projects for my studio.  Paintings, drawings,
administrative tasks, repair and studio related research materials.

home-projects.org
Just that.  Anything related to the house, cars, wife, kid, dogs, etc.

notes.org
I use this file for random thoughts and information I find online.

mind.org
How to explain this one? When I find information that I want to act on in
the future as R&D I throw it into mind.org and
give it a todo status.  Usually stuff in here pertains to things I don't
understand and want to spend time learning.  Hence the name.

phone.org
When on client calls I take notes in the phone file which later gets refiled
to their respective places

calendar.org
This is synced using Doug Hellmann's ical2org python script.  I have a cron
set to sync it every hour so
that my google calendar updates my org file.  I have todochiku installed to
notify me via growl of appointments.



I may go back to having a single org file for each client.  Right now I have
about 20 projects in that file with long lists and
I'm struggling a little with keeping it organized enough that I don't lose
track of projects.

Beyond this setup, every hour a cron syncs my org files to a private
mercurial repository at bitbucket.


— Greg