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I'm not an academic either, and a few months ago I dumped Evernote in favor of DEVONthink Pro Office. Couldn't be happier.

You can reference material in DEVONthink by selecting Edit->Copy Item Link and then pasting that link into the note field in OmniFocus. The cool thing is that if the linked document is synced via DEVONthink To Go on your iPhone/iPad, the link also works there too (i.e., clicking the link in OmniFocus for iPhone/iPad opens the document in DTTG all on your iOS device)!