A little know fact is that the iPhone can indeed send/recieve serial data through the dock connector(jail broken of course). My idea is to interface the iPhone with an xbee and have commands that can be executed with a tap of a button. Eventually mission planning could be implemented in order to Remove the need for a laptop in the field. Any comments? I estimate $30 in hardware costs to connect the xbee to the iPhone. 
Andrew

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Well, no replies but I have made a ton of progress! I wrote a simple app that allows me to send data over serial and it is working beautifully! Next step is to figure out how to send commands over the xbee to the ArduPilot

Sounds good. I'd like to use my iPad for a ground station some day. It makes more sense than a laptop. I'll just need to wrestle it back off my kids.....

Good news I developing a app for iOS so we can use the regualar xbee shield and xbee to send receive data with each other. I am working with google earth to make it possible to set waypoints with the apm. Once I receive it in the mail. (First batch I hope) to do some testing with my bixler then with quad. This will elimatnate the laptop completely. If you have any questions or found a better exploit feel free to share. This will work with iPad 1, 2 and 3GS, 4, 4s. You will most likely will need iOS 5.0 to use this app once I publish it. It will be publish I tunes next month and Cydia to.

How are you planning on communicating with the xbee? The only way I can think of is through the serial pins of the iPhone and that requires root level access. You said that you were planning on publishing through iTunes, did you find another way to communicate with the xbee?

Anyways, I plan on buying an xbee pair within a few weeks and making sure I can communicate between the two. Then in a couple months when I get out for the summer and start my job i'll have enough money to buy the ardupilot and throw it in my rc plane. 

Right now I am using apple camera USB port and FireWire cable to arduino UNO to xbee 900 pro. I might do a pcb board or find a good off the shelf. So far no jailbreak has been used but I think I might have to later on waypoints and returning telemetry data. If Apple rejects the program since I am not changing anything in root I just send it Cydia only. Plans are still towards iTunes store. Data streams are funny with arduino but are easy to follow. I looking at the telemetry firmware with ardupilot and copter so waypoints and firmware loaded is the same so if you use ous device and computer at the same time you get same information of data. Sorry typing on iPhone.

This is my very simple application to send serial over the iPhone's 12 and 13 pins. The advantage of this method is that it would not require a separate microprocessor to send the serial data, instead the iPhone would do all the calculations and could even power the xbee.

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Also, since i don't have the ardupilot yet, i'm still fuzzy on how to xbee communication works. I know its serial but is there like a list of commands?

I did find this though:

http://diydrones.com/profiles/blogs/ardupilot-telemetry-protocol

Assuming you will use the Mission Planner, all of the mavlink commands that are passed to and from the APM over xbee are dealt with behind the scenes.It's all point and click.

my bad, i should haver read the initial post more attentively. There is a full list of mavlink protocol commands somewhere in the wiki: http://code.google.com/p/ardupilot-mega/

Thank you very much!! Knowing that the protocol is called MAVlink saved me a ton of googling! I did find a MAVlink library that I will try to implement into my app ASAP.

Here is the library btw:http://qgroundcontrol.org/mavlink/start
Re you using FTDI cable to iPhone only? If you can get that work then you might be able port mission planner mavlink.

Kinda, but i had to write the "drivers" for the iPhone so that it can handle the UART serial data.

As you can see, I connect the "tx/rx" cables to the iPhone pinout along with the 3.3v and gnd. this allows me to communicate and power the arduino. I will eventually switch it for an xbee.

Also, have you gotten MAVlink to work on the arduino? I don't really understand the protocol at all.

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