The USB connection is a Serial port over USB that is used both for programming the board when the bootloader is active and for "normal" serial communications when your sketch is running, using the Serial object predefined in the Arduino/Wiring toolbox.
So, Yes, any program that can read and write to a serial port on your PC can be used. You can code this in Java, C, C++ or Python. There are several discussion threads on this forum about this topic.