It seems gnome-shell (3.6.1) maximizes large windows. I.e. if the last non-maximized size for a window was large, the application will open maximized next time.
I've head of such a thing in Unity, but I'm using Gnome 3 with (to the best of my knowledge) no window manager other than the shell. All my searches show up tips that involve either Unity, metacity or compiz settings, and gsettings list-recursively shows no setting that looks pertinent.