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This response is a very Devon Think biased (at least to start with), but here goes. DT (or at least DTPO - which I own) offers a GTD template that might give you an idea for how to organize each DT project database that you create in a GTD-friendly manner. I create a database for each area of responsibility and for each major project. I have also modified the template for my general use GTD trusted storage system (not much change was really required).

That said, I am not terribly concerned with mirroring the structure of kGTD (and hopefully OmniFocus) with any of my DT databases. Because of the relative granularity of my DT databases (and DT's great search tools), I don't feel any need to try to exactly match the structure of DT databases with kGTD.

I am hoping that I'll be able to automate the process of feeding notes between the OmniFocus and DT. It most definitely would be useful to autoarchive completed OmniFocus projects to DT.

We will have to see if hooks are there to do stuff like this.