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I tend to keep these kind of "status update" notes in the the note fields of my projects and actions. I just prepend each entry with the current date and time (In OmniFocus, go to Edit -> Insert Time Stamp -> Short Date and Time, or hit Command-|), followed by whatever status notes I want to add. Sometimes I'll even make the time stamp bold so it stands out a bit more. For example:

6/15/09 1:30 PM - Looks like marshallj asked some interesting questions about OmniFocus that I'd like to think about. Maybe I'll post a response later.

6/15/09 2:01 PM - I posted some ideas on the OmniFocus forum.
I like this approach because all those notes then get preserved with my actions and projects in my OmniFocus Archive file. This makes it very easy to reconstruct a project I completed months ago and see exactly what happened and when.

I also like the fact that the status updates get synced to OmniFocus on my iPhone as well. I can add/review updates from anywhere.

As for other project support/reference material, lots of people use a database app like DEVONthink or Yojimbo. But I've personally found the Finder and Spotlight to work well for my needs. It's robust, easy to transfer to another system, and allows me to use whatever file format or editing application I want to modify the files.

Of course, different people have different needs, so ultimately you should use whatever works best for your specific workflow.