Other than initial size and position, window control like this is usually handled by the window manager, not the program or the shell that launches it. KDE, for example, has application-specific settings ability, accessible through the window menu or system settings.
There are ways for the shell to talk to the WM, however, such as through dbus.
xdotool is stand-alone program that sends simulated input events from the shell to the X windowing system. Unfortunately, it can't directly handle window raising or lowering, but you can simulate a press of a hotkey combination, which is what macemoneta's example above does.
However, his example may affect all open windows of the program. To be certain you're affecting only the one you're just launching, create a wrapper script like this:
#launch the program in the background, with all command-line options passed to it.
firefox "$@" &
#grab its process id.
#wait for a second so that the window has time to fully register.
#use xdotool to make sure that window is raised to the top.
#this is necessary because it won't directly accept xdotool keypresses otherwise.
#matches both the pid and the class, to ensure we have the right window.
xdotool search --all --pid $pidno --class firefox windowactivate
#use xdotool again to simulate your hotkey combo. Adjust as necessary.
xdotool key alt+F9