I was able to use the 'xdotool' under Ubuntu 11.04 beta, but the 'selectwindow' was not a valid command, I had to hack a script with:

$ while true; do sleep 1; xdotool getactivewindow; done

then watch the window ID go by while I selected the window I wanted, then decoded the responsible PID with:

$ xdotool getwindowpid <the-window-id>

I was able to use the xdotool under Ubuntu 11.04 beta, but selectwindow was not a valid command, I had to hack a script with:

$ while true; do sleep 1; xdotool getactivewindow; done

then watch the window ID go by while I selected the window I wanted, then decoded the responsible PID with:

$ xdotool getwindowpid <the-window-id>