I've written about this problem in org-mode, the emacs outlining and organization tool that I us, before, but I'm readdressing it for my benefit as well as yours.
Org mode is an outlining tool, fundamentally. It provides a nice interface for editing and manipulating information arranged in an outline format. Additionally, and this is the part that everyone is drawn to, it makes it very easy to mark and treat arbitrary items in the outline as "actionable," or todo items in need of done. The brilliance of org-mode, I think, is the fact that you spend all your time working on building useful outlines and then it has a tool which takes all this information and compiles it into a useful todo list. How awesome is that. For more information on org-mode, including good demonstrations, check out this video.
The problem is a common and recurring one for me. I basically live in the agenda mode--that compiled list of todo items--and I don't so much use org-mode for making outlines. Truth is, I have a "Tasks" heading in most org files, and I use the automatic capture option (e.g. org-remember) to stuff little notes into the files, and beyond that, I mostly don't interact with the outlines themselves.
This isn't a bad thing, I suppose, but it means that org-mode can't really help you, and you've short-circuted the ability of org-mode to improve the organization. Under ideal circumstances, org allows you to embed and extract todo lists from the recorded record of your thought process. If you're not actively maintaining your thoughts in your org-mode files, it's just another todo list. That isn't without merit, but it doesn't allow the creation of tasks and the flow of a project to spring organically from your thoughts about the project, which is the strength of org mode.
Intermission: I took a break from writing this post to go and reorganize my org files. What follows are a list of "things I've been doing wrong" and "things I hope to improve."
I don't think I had enough org-files. There are lots of approaches to organizing information in org: one giant file, lots of small files for individual projects, a few mid to large files for each "sphere" of your life.
Initially I took the "medium sized files for major ongoing projects." I had a writing file, and a work file, and a writing file, and files for the fiction projects that I'm working on, and a notes file, and a clippings file, and so forth. Say about 8-10 files. It works, but I think the thing it did was it caused me to use the org-remember functions to just dump things in a "tasks" heading, and then work from the agenda buffer, and not ever really have to touch the files themselves. Org files need to be specific enough that you would want to keep them open in another window while you're working on a project. I think the point where you know you've gone too far is when the first level headings start to replicate organization that might better be handled by the file-system.
Use the scheduling and deadline functions to filter the todo list into something that is workable. It's easy to just look at the task list and say "oh no, I don't want to work on this task right now because it depends on too many things that aren't done, and there are other things that I could work on." Scheduling an item, if not setting a deadline, forces me (at least) to think practically about the scope of a given project, what kind of time I'll have to work on it, and what other tasks depend upon it.
When you're using org to manage huge blocks of text--or any system, really--it can be difficult if you have multiple hierarchies and depths of greater than two or three. It just gets hard to manage and keep track of things and figure out where things are, particularly given how useful and prevalent search tools are.
Having said that, When you're organizing tasks in org, that limitation, one that I find myself imposing upon myself doesn't really work terribly well, and leads to files that might actually be more difficult to read and to work out of.
I started using the "org-archive-subree" function for archiving content when I was through with parts of the outline, This sends the archive to a separate file and while it works, I find it... less than useful. I've since discovered "org-archive-to-archive-sibling" which is a great deal of awesome, and I recommend using it exclusively.
Write content in org mode when possible. Though some people (hi Matt!) are keen on using org as a publication system, I'm not sure if this is the right answer, but I do think that its good during very creative phases of projects to do the work in org, mostly as I think it facilitates focusing on the current problem (through collapsing of the tree to show you just what you're working on,) and also for working non-linearly as you can leave yourself TODO items for later action.
At the same time, if you tend to maintain org files that contain planning for more than one project, I find it cumbersome to also draft in these files. So I think "keep smaller very focused org files, and maybe do drafting in them if appropriate."
That's a start at least. I've made these changes--which are really quite subtle--and I like the way it feels, but we'll have to see how things shake down in a few weeks. As much as I want to avoid tinkering with things--because tinkering isn't the same as getting things done--I really do find it helpful to review processes from time to time and make sure that I'm really working as effectively as I can.