I use a more lightweight form of GTD for work. I have been doing this for about 4 years now. It has worked out really well for me and I encourage everyone to check out David Allen’s book and give it a chance. It is not difficult or complicated and it really helps to keep things organized.
I have used the lightweight, ruby based wiki Instiki instead of paper lists for the majority of the time that I have used GTD. Unfortunately, my Instiki started becoming pretty large, (I used it for meeting notes, and other things also) and in a couple of instances it had a problem resulting in data loss of a few weeks. After it happened the third time, I threw in the towel on Instiki and made a change.
For the last few months, I have been keeping all of my GTD lists and notes in html files. Writing everything in a markup language is not a big deal for me. In general I find I only need to use four or five tags most of the time anyway. I create a new file every week that is named for the date range of the week (Ex: May5-May9). The files are stored in a folder named for the year (Ex: 2008). I copy the previous weeks file to the current week every Monday morning and use it as a starting point. I use my web browser to read the files and of course GVim to edit the files.
The only concern I had with going this route was how to search through the files on a windows PC, Instiki has a search box that made it easy. Since I installed Cygwin for some other things, I remembered that grep is part of it. Grep is probably better than Instiki’s search anyway so I have been using it to search, and of course it works like a champ.