Ideally, you'd want to generate those different plots using subplot.
Your exact question has been answered by ZiV in the mathworks forums:
One way to do this is to extract xdata and ydata from existing figures, then re-plot these data in a new figure window as desired. For example,
open('gugu.fig');
h_gugu=get(gca,'Children');
x_gugu=get(h_gugu,'XData');
y_gugu=get(h_gugu,'YData');
open('lulu.fig');
h_lulu=get(gca,'Children');
x_lulu=get(h_lulu,'XData');
y_lulu=get(h_lulu,'YData');
figure
subplot(121)
plot(x_gugu,y_gugu);
subplot(122)
plot(x_lulu,y_lulu)
saveas(gcf,'gugululu','fig')