As a two-monitor user at work, I\'ve noticed that applications behave differently with regards to what monitor they open on (primary or secondary monitor, the last monitor the a
From traditional Unix and Linux window manager perspective, you don't control. The window manager handles the positioning of the window.
You may be able to give hints to the window manager, but it should be possible to configure window manager to ignore such things. Moving or placing the window from the program can easily cause pain when a big virtual desktop is in use.
See: http://standards.freedesktop.org/wm-spec/wm-spec-latest.html