Have a look at the Motherboard arduino code xybot.ino. In it you will see the GCode and MCode commands the software currently handles.
If you are going to write your own application to send these commands over the USB serial link, be aware that the motherboard sends serial information back to the host PC as well as receives it, for the end-stops, and also sends an OK after processing the command.
I have added stuff to my code, but a quick check on an earlier version of the xybot.ino in my project archive shows:
G00 and G01 both implement a move to the X Y coordinates with additional processing of F for feed speed and A for dwell, G28 implements the home function
M01 with a following number sets the servoe for the pen to that position
M02 does pen setup for U up and D down position
M03 sets the delay to the following number
M04 sets the laser power to a following value 0-255
M05 is for the setup method
M11 tells the motherboard to report the value of each of the four end-stops
As an example of the sort of thing you can do by editing your arduino file, I have amended my code so that G00 lifts the pen and turns off the laser then does a fast move to the coordinates at maximum speed.