I would love to be able to let my iPhone-App communicate to my Arduino over Bluetooth. I found some Bluetooth shields that support the following protocols: BCSP, DUN, LAN, GAP S
So I don't know how to implement, but I think your Arduino should simulate an Bluetooth Headset and let the App parse the data. Because iPhones only support Bluetooth Headsets this would be one of the only methods. And it would be very hard.
I recommend you to do things like this over Wifi with an Wifi-Shield. Than you could use Apples genial bonjour
systeme, to automatically detect your hardware.
Hope that gives you some idea, how to solve the problem,
Leo