Last year I wrote a VB application to interface with the IFI mini-RC. The GUI has four "virtual" joysticks and 8 bits of input and received 8 bytes, 6 signed ints, and 16 bits of feedback from the robot. Once you get the program installed on the RC you can drive the robot around using your mouse. It also captures and plots up to ten of the IO channels. You can download it, and the program from the RC, from
http://members.cox.net/seanwitte. I've posted this before but its been awhile. If you look in the pc_interface.c source file you can see the information being exchanged. The protocol is weak and blocks while its waiting for data.
I wrote that before I had a buffered serial port library so its a synchronous protocol with the PC. There isn't any error checking and it will crash the RC if you unplug the serial cable while its running.
If you design a standard serial protocol then people would be able to use it with any programming language. If you wanted to be really flexible you can design a framework that wraps all of the IO and loads "virtual robots" as modules at runtime. Sort of the way RoboCode works. Once you standardize the code running on the RC anyone can build a client framework to take advantage of it.
I know this is a thread about using Linux, but there might be a few people who would like to use Windows (well, maybe just me). For that I would implement the framework as a standalone exe and load the robot classes at runtime.