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If you can collect all data with internal sensors (sound, image, motion, etc.), then you can do all software and all Java. However, if you need external sensor inputs, it gets more complicated.

Most Android phones are USB device (slave), and as such, cannot initiate external triggers and/or events. So, you would need an external controller to collect data and "ADB push" into the phone. Android Debug Bridge (ADB) is a standard protocol in all Android phones. We are using a PIC24FJ256DA206 to do it.

You can have a Java App talking to a socket server or just polling some data location in flash memory. Furthermore, you are likely limited to user space access, without doing too much damage to the phone. We have gained temperory root access to a LG VS740, but it won't survive reboot. Making permanent root access risks bricking the phone. So, we are not there yet.

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Well, you could build something discriminate 'stepped' audio frequencies anda few photocells could detect lit areas of the screen. But yeah, not the same as digital I/O or serial out.

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It also occurs to me, you should be able to emulate a modem with an Android phone.

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Yes, if you provide the driver.

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Only if the OP plans to put a Desktop/Laptop/Tablet there. If so, he could just use the native ADB interface, instead of a modem interface.

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There's always a catch.....

I just installed the Android SDK on a 32 bit laptop. To say it is slow is to be understated.