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- In mail, right click anywhere into a specific email you want to clip (not selecting anything, just right-click into it)
- In the drop down which comes up, go to "services".
- Find and click "OmniFocus: send to inbox" (or similar), click it.
- In Omnifocus, check your inbox. There should be a new task named after the subject of the email. When you open that task's note field, the entire Email (formatted and everything) should appear in said note field.

Does this work for you?

Note: If you recently upgraded from Snow Leopard to Lion it may be that the upgrade automatically disabled clip-o-tron. To make sure, go to OF's preferences, "clipping", remove and reinstall clip-o-tron.