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The iOS 5 update appears to sometimes turn app icon badges off - which apps this happens to seems to be somewhat random. We're seeing other developers report the same issue with their apps; hopefully it'll get fixed in a future iOS update.

The fix jjlucsy recommends should take care of it, though. Just open Settings on your phone, tap into Notifications, then make sure OmniFocus' "Badge Count" setting is set to "On". (Ditto for any other apps affected by this.)