For example, say I wanted to start gnome-terminal with it's northwest corner at 0,0, and make the window 736x434 pixels (apparently the default, which allows for an an 80-character by 24-character terminal window).
I'm not sure how much of this matters, but I'm using Ubuntu 11.04 with GNOME 3, and whatever versions of Xorg and the window manager (metacity? compiz?) come with that distro.