Below is infodump on how I use org-mode personally.. You are welcome
to poach ideas. Generally I'm pretty happy with my setup, and do not
plan to do any radical changes to it. Wall of text warning.

1. Org file per project, with single top level heading.. Each file has
   a #+TAGS cookie that assigns default tags.

   Such project files would have more then one level heading, usually
   when project logically splits into sub-projects

   Example: Emacs.org, top level headings. This one has unusually large
   amount of top level headings.
   
   - Emacs 
   - Org-Mode
   - Paredit-Magic
   - C-Paredit
   - Cycle-buffer

A few special org files which are not projects, one is called Assorted
Accounts for recording acc/pass/email info on various accounts, and
one is called Assorted Info for basically a knowledge base of anything
that is not a TODO. The way I access these are through C-c / search,
seems to work very well.. Another "special" project is Finances.org
and has everything to do with investments, encrypted entries for all
financial accounts, all recurring TODOS for bills, or portfolio
review, investment ideas, spreadsheets etc.
   
Capture often. Write down just enough so you can re-construct idea
later.. If you often wondering "wtf did I meant by that, then you are
not writing down enough.. If possible write/assign yourself a shortcut
key to your window manager so you can capture a short sentence with 1
key stroke even when in the other programs.

If it takes less then 1 minute to do what you are capturing,
especially if it involves emacs customization, do it right there, and
mark it it done, or C-c C-k it.. I usually mark it done and C-c C-c
it.

All captures go to Mind-Sweep.org, under top level heading.. Every few
days (once I have 10-20 items) in there, I go ahead and refile them to
appropriate projects, assigning priorities and efforts if these are
not there.

Have two agenda keys to show agenda sorted by priority, and by effort
up..I use block agenda that shows day agenda first, then all NEXT
items, then all TODO items.

Learn to use / key in agenda to quickly filter out stuff by tags.. For
me /e switches agenda to filter out be :emacs tag.

Have areas of focus. The mind is like a process working set. If I had
been working on some emacs problem and have Emacs "booted up" in my
brain, it takes a while to switch reboot my brain into "Looking at my
investments mode".

So as long as I'm working on lets say fixing something with paredit,
you can just as well knock out some other emacs things..

That is where agenda sorted by effort comes up. Since I'm hacking on
my emacs setup anyway, I bring up my effort-up agenda view, filter by
"emacs" and just knock out every item estimated at 10 minutes or
less. Sometimes knocking out up to 20 or so small TODO's in 2 hour
burst, taking care of everything that was annoying me with Emacs in
last 2 weeks.

Assign priorities to prune aggressively. If you have that #A item
starting you for last 5 days, its not #A.. Demote it until it sits in
the #F pile way down in agenda.

Temporary move projects out of agenda. Lets say you have a well
defined project and a bunch of nicely prioritized items, some of them
#A (which they are in the context of that project) but right now you
just don't feel like working on that project.

Starting at these #A items on top of your agenda every day without
starting to work on them, may be demoralizing. Way I deal with it, is
that I have "hold" tag, which I put on top level headings of the
projects, and its excluded from my agenda by default... If you have
not touched a project for 2 weeks, it probably should be on
hold.. When you bored and looking for things to work on, they you can
use agenda view without filtering out the "hold" projects, and see if
you can get a start on some of them.. This way I have only 3-4 projects
that are "in focus" rather then 30.. 

Review low priority items once a week, if you remember reviewing that
item last few weeks, just delete it.. If you are type of person who
can't let go, move it to MAYBE state.

If something computer related annoys you and interrupts your work flow
often, it should be #A item and needs to be fixed. Ie if you Emacs
session consists of 50% beeps, you need to fix something in your
setup.. If you dread doing something because its just too much effort,
you need to automate/rethink/change that process.

Don't burn out.. The bodybuilders and athletes have it right, you have
to cycle. If you go 100% all the time, generating ideas and knocking
out TODO's like a robot, you'll burn out. Take it easy for 1 week each
month. Does not mean eat pizza and party every day, but basically its
"relax and don't kill yourself" time.

Do any health, work, and lifestyle related TODO's first over any
computer related ones. Get that physical. Update/re-balance those
investments Deposit them checks and pay them bills. Switch to online bill
payment for everything, and synchronize your bill cycle dates, so that
you can pay all your bills in 30 minutes once a month.. If company
offers automatic billing feature, use it.

I have a "Pay bills" monthly recurring TODO, with 7 checkboxes. Of
which 4 pay themselves with automatic bill pay, and are checked
when I receive saying "your bill had been paid", and it takes me 10
minutes to pay the rest.

My stats if you want to compare:

Number of projects: 37
Number of "hold" projects 31
Number lines in all .org files: 16000
Number lines in all .org_archive files: 20000+
Number of TODO: 350
Number of #A todos: 8
Number of #B todos: 21
Number of #C todos: 30
Number of #F todos: 100 or so

Most important tags I have:

  focus   <- set on projects i should be working _right_now_, kind of opposite of "hold". 

  emacs   <- stuff to configure/fix in emacs

  hold    <- projects on hold

  bind    <- todos "bind some key to do whatever" which I have a lot of

  browse  <- todos "check out X, or research X on the web". Use this
             when you feel like browsing the web, can just as well
             make web browsing useful, instead of going to "waste your
             time" sites like reddit.
 
  health  <- any health / fitness related stuff

  finance <- investemnts, payroll, salary, bills

Plus private tags for various projects, which only make sense in the
context of the project

At Wed, 14 Sep 2011 10:43:28 -0700,
Alan E. Davis wrote:
> 
> I've been using org-mode for a few years.  My agenda is cluttered with tasks that are weeks and
> even months past due.  I am "this close" to declaring "orgmode bankruptcy" and starting from
> scratch, except my current setup works so well for other things.   Might still do that, but I want
> to ask for ideas. 
> 
> I stumble consistently over the distinction between projects and tasks.  I think there is not
> clear distinction, but I need to find a way to organize them so that, at least, agenda displays
> the day to day TODO tasks separated in a meaningful way from the long term projects that I need to
> remind myself of (and there are dozens of these).  
> 
> PROJECTS: I can define projects as
>        - an overall series of tasks related to a single purpose
>        - a recurring task (monthly calendars that I need to remind myself to make each month)
>        - an actual project I am working on (writing a proposal, or a research project about a
> coral, or a recipe database, or reconstructing a LaTeX file tree for a publication ten years ago)
> 
> TODOS: perhaps tasks could be anything,
>       - bills (marked by tag "bill"
>      - phone calls to make
> 
>      I am starting to understand how I TODOS can be scattered through all my other files.  
> However, the greater the number of agenda files, the greater the clutter.   And, as a recent
> thread called to mind, there are times when the list of agenda files prevents me from searching
> for tags or todos.  SO where is the happy medium?
> 
> Some thoughts:
>      -  I tried to write a custom agenda command that defined the agenda files to encompass all
> *org files in a directory.  This actually set the agenda-files variable to all files for the rest
> of the session, so I gave that idea up----although I know it's possible to do it. 
>      -  Again, the number of agenda files seems to be constraining. 
>      -  There seem to be issues between defining the agenda files explicitly, or adding them one
> at a time.
>      -  It would be useful if agenda searches automatically picked up the recent files I had
> worked on during the session,
>         however, in as streamlined a way as possible.
>   Â> 
> I don't need to be reminded everyday that I have to organize bibliographic references for my next
> trip to the library, but I have to have a way to keep these organized to jog my memory in planning
> my time in some loose sense.
> 
> I do need to have a list of bills that I can access without having to sort through the list of
> projects that are 3 months overdue.
> 
> Almost every week I have new insights into how to use tags, so perhaps I need to junk alot of the
> tags I set up long ago.
> 
> These thoughts are somewhat disconnected, and I apologize for this. 
> 
> And I would be grateful for any comments that would shed light on how to solve these issues. 
> 
> Alan Davis
> 
>