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I just realized I never followed up on this. I am using iNotes now via Safari. The clipping works fine with iNotes. When you first open an email, it is a Lotus Notes Tab. There is an icon in the upper right to expand the email into its own window. Once you do that and enable >View>Toolbar, you'll have revealed the unique persistent url to the email. Highlight it and use the service menu to clip it into OmniFocus. Works great. You can then file away the email to empty your inbasket. Later on in OmniFocus, clicking on the url will get you back to the email, even if iNotes isn't running at the time.