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Here is a nice workflow that I have used with great success for some time now that I thought would be a good idea to share with others.

GTD states that you should have a folder cabinet with supporting materials for your projects. Now, I am zero low-tech so for me that would be a directory on my computers desktop. The problem I need to deal with is that for some projects at work I receive multiple files from different sources that are all related to the project itself. This is how I deal with that.

* I keep a folder on my desktop called "Projects Support Materials".
* For each OmniFocus project (that needs it) I create a folder with the same name inside this directory.
* In the OmniFocus project's note section I create a link to that folder so I can open it from within omnifocus.
* Sometimes I create links to each supplemental file/email inside omnifocus so I can open them directly with e.g. quicklook. I write small descriptions next to their icons like "Letter from X regarding Y".
* Whenever I gather a file (regardless of source) associated with the project I drop that inside its "Project Support Materials" folder.
* When a project is finished/dropped I move its corresponding directory into a folder called "Archive".

This allows OmniFocus to become a hub for any information related to any of the projects going on at work. Instead of thinking "where did I put that document" (navigating) or what did I name that document (spotlight) I can just go into omnifocus and get a birds eye view of my project resources.
And, I have zero loose files on my desktop!