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This quick tip is for Gnome users. I always wanted new windows to start centered on the desktop but never searched for something to modify this behavior. But yesterday I stumbled onto something which fixes this by changing 2 parameters in Gnome's almighty gconf editor:

Press Alt+F2 and enter gconf-editor, then set the following two values:

Key: /apps/metacity/general/focus_new_windows Value: smart
Key: /apps/compiz/plugins/place/screen0/options/mode Value: 1

Now your applications should start up nice and centered.