I promised I'd blog about which tool I ended up using to get organized and how I got there. I'm not going to go through all the details and background but I will focus on the two that work out the best: Journler and Circus Ponies Notebook.
Both are truly wonderful programs. The big difference here is Circus Ponies Notebook uses a notebook metaphor - it looks exactly like a notebook including you can make it look like a spiral bound notebook, a yellow legal pad, or even Cornell Notes. The problem here is trying to make a computer program look and act like a notebook ends up being a tad on the clunky side.
After trying Journler, I switched. It makes use of the features a computer provides: searching, indexing, categorizing, and tagging. You can do folders and smart folders. I call it "iTunes for my life". The folders are like playlists of the information you want to organize - you just drag 'n drop your stuff and it is there. The smart folders are like smart playlists - define the search criteria and anything that matches just shows up there.
Now if Journler just did todo lists better, I'd be using it for everything. I wonder if you could somehow combine Journler and iGTD.