I don't think it is a good idea to mess around with system defaults, especially if someone else is going to be using your machine. Maybe this is my cop-out way of saying that I don't know if this can even be done, but I'll propose a workaround anyway.
Say you plot some stuff:
figure(1)
plot(rand(10,2),'g')
figure(2)
plot(rand(10,6),'g')
hold on
plot(rand(10,5));
Then you could change the green stuff to your own version of green by just adding this line:
set(findobj('color','g'),'Color',[0 0.5 0]);
