As far as Android phones are concerned, I know there is one guy out there who has made an application that connects (I believe) to the microphone input (via a special mini-b extended USB plug; probably something you have to custom mod yourself from a headset) to give you an "audio oscilloscope" (it doesn't work with digital signals). This is close to what you are asking, albeit only a single channel.
As far as what you are asking, this is the problem: both devices are (currently) USB slaves. I believe that in API discussions, though, there have been talks about allowing the API for Android to use the USB port as a master, but I don't know what work has gone on there (I don't follow it that closely). I think, though, that it has been an issue of the API and access, more than any device limitations of the various Android phones.
There is also the possibility of using bluetooth; I know that they recently (?) released the API for bluetooth capabilities on the Android SDK - so (in theory?) you could set up BT on the Arduino, and communicate wirelessly with it using the API.
My main interest has been the idea of creating a (likely) low-speed multi-channel digital signal analyzer (likely a single port of 6 bits) and use the Android SDK for the logging and GUI; the opening up of using BT makes it even more attractive, since you could monitor something wirelessly (say a circuit on a mobile robot). Regardless of the application, though, what is ultimately needed is some way to get a high speed serial link with the phone; once that is done, you could plug anything you wanted into the Arduino, and monitor it (with appropriate software, etc on both ends).
Lastly - there is also the idea of communicating over 802.11x (would make the Arduino end a tad expensive)...
As far as the iPhone or other smartphones are concerned, I don't know what the capabilities are there, but I would think things would be nearly the same (or perhaps more advanced; I have heard that the iPhone's SDK audio processing capabilities are far better than the Android SDK - mainly less latency, from what I have read - given the head start of the iPhone and its maturity, other interfaces might be more easily worked with)...
