First off, since I'm not an emacs user yet, some of the key binding issues have slowed me down. Out of the gate I have set up my projects in a simple, and I think, logical fashion. I've read about other people maintaining a single .org file with their entire life in it, but that seems a bit too unwieldy to me. Perhaps that's my lack of emacs skills showing through though.
In my initial setup, I have a .org file for each project. Projects that are work related are simply named work_
For my non-work life I have a life.org file. I keep this file out of the global TODO list and use it stand alone for everything from what needs to be done from things with the house to buying gifts to whatever ("TODO cancel XBOX live subscription" is on there).
Finally, personal projects have their own file, projects.org.
The beauty of org-mode is that it's just text files. At any point and time while taking notes on a project I can type "TODO" and the line becomes part of the global TODO list. The list lets me jump right to the TODO line and see the context of the notes that caused the TODO to come about. Something so simple, yet at the same time completely awesome.
This is the first time in a long time I've been excited about something like project management. I'm not really surprised that emacs contained org-mode (isn't emacs it's own self hosting OS by now?), but at the same time I never thought to look. The org-mode website mentions converting vi users to emacs. I can't say that will happen, but hopefully learning both vi and emacs to a sufficient level will not be like crossing the streams.