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You might also try Journler: <http://journler.com/> It may not have every feature you seek, but it has many more features than Yojimbo. (I own both.) Also, see David Chartier's great podcast, introducing Journler: <http://www.tuaw.com/2007/05/24/tuaw-podcast-24-journler/>

I do understand what you want: You want a cross between OmniFocus and Yojimbo (or between OmniFocus and Journler). While I understand your desire to have everything in one place, I'm not aware that any apps are doing that, just yet. Journler and Yojimbo help you manage and organize documents and information, while apps like OmniFocus and iGTD (oops, did mention the i-word?) are about managing your projects and your time. (That's an oversimplification, but you get my drift.)

One way to look at it is this: It would be impossible for OmniFocus to incorporate every function that every project requires. While your projects may require documents and custom columns, someone else's projects may require work in iTunes or iPhoto or Word. Well, we can't expect OmniFocus to become a music player, a photo organizer, and a word processor, too, can we? Of course not. I think OmniFocus should do what it does best -- help you decide what to work on next -- and then, as you focus on a particular task, you should switch to the appropriate tools for that task -- whether that means another computer program, or your sewing machine, or your circular saw. OmniFocus isn't meant to replace your *tools*. You'll still need tools to get things done.

For you, perhaps the best tool is Yojimbo, or Journler, or File Maker Pro. Only you can say for sure.

Also consider an app like QuicKeys. I have custome shortcuts for every app I use, so switching to Journler or Safari (or whatever) is no different than switching, within OmniFocus, from Project view to Context view. Control-J puts me instantly in Journler, and Control-O puts me instantly in OmniFocus. Once you've defined your custom shortcuts, switching between programs is so effortless that it's literally no different than switching between two windows within one program. Once the effort has been eliminated, you'll never know the difference. (Well, you'll know, of course -- but it'll be so easy that you'll no longer care.)