Is there a way close applications gracefully from command line (the "kill" command is no good since closing with it will not make the application save its state for next launch).

when closing with the "X" on the application's window, the application saves its last state (someplayer, xournal, etc...) - i want to simulate this close command by command line.

i've seen it is possible to launch application by using dbus:
dbus-send --type=method_call --dest=com.nokia.HildonDesktop.AppMgr /com/nokia/HildonDesktop/AppMgr com.nokia.HildonDesktop.AppMgr.LaunchApplication string:[appname]

but by using d-feet i've seen that this is the only available method there and that there is no "CloseApplication" equivalent...

The standard kill command should work. If not, it's a bug in the application - it should exit gracefully after receiving a SIGTERM (going through the normal exit routine). It's a SIGKILL (kill -9) which should force it to exit immediately without saving state.