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The problem I see with trying to store reference information within the completed projects in OmniFocus is that eventually you're going to archive the old projects to an offline database. Once you do that, finding the reference material is problematic. Besides, searching in OF just isn't as flexible as in the tools designed for information storage and retrieval. I think most people agree that using an external tool for information and files is the way to go. DEVONthink, Yojimbo, EagleFiler, Together, Evernote, OmniOutliner, and even the Finder are some of the more popular options.

One of the features that helps integrate OmniFocus projects with these tools is the ability to use hyperlinks to directly open a task or piece of information. You can add a link in an OmniFocus task that references a document in DEVONthink. When you click on the link the document pops up. You can also add a link in the document's attributes that references the OmniFocus task. Click the link, open the task. This two-way reference ties the two tools together quite well while letting each tool do what it does best.

As for keeping it all in sync, OmniFocus does this better than anyone at the moment. DEVONthink is currently working on syncing between Macs but also has a built-in web server that can serve up information plus a universal iOS app. Yojimbo syncs with MobileMe and doesn't seem too interested in doing it any other way though it also has an integrated web server for sharing data that works well plus an iPad only app. I'm not sure what the state of EagleFiler is but knowing the developer I'd be surprised if it's not on his radar. Evernote is all about syncing since it's "cloud" based. Finder can make use of Dropbox. The rest I don't know.