How can I determine what application is asking "Where is GrowlHelperApp.App?"
You could have used sudo opensnoop to see what files are being opened or fseventer to see what files are being modified.

Those dialogs are often shown by AppleScripts that have reference a missing application. You could also have tried running mdfind GrowlHelperApp, but it doesn't search the contents of compiled scripts or scripts saved as applications.