Protocols used to talk between an embedded CPU and a PC

Question

I am building a small device with its own CPU (AVR Mega8) that is supposed to connect to a PC. Assuming that the physical connection and passing of bytes has been accomplished,

Answer 1

Modbus might be what you are looking for. It was designed for exactly the type of problem you have. There is lots of code/tools out there and adherence to a standard could mean easy reuse later. It also support human readable ASCII so it is still easy to understand/test.

See FreeModBus for windows and embedded source.