In most configurations users can shut the machine down, using the gnome menu. This lacks a command line interface. 
I want to be able to open a terminal and do:
wget htt:p//a_big_file; gnome-logout --shutdown
or something similar.
Il will be useful also using sleep xxx && gnome-logout --shutdown
As of now you have to be root to do that, and it closes the session badly.

I do shut my computer down automatically very often and this is the major annoyance I have in gnome.

I also suggest a small applet or utility to implement a shutdown timer.
It will also be useful to integrate shutdown capability on some other applications, e.g. "shutdown when tranfer/encoding/burning/scanning is finished.

KDE has a kshutdown program, gnome should have something similar too. 
However I cannot stress to much the need for a command line interface to session closing and shutdown. So it is better to create a command line tool and make programs that integrate shutdown capabilities use that command, instead of the magic way gnome uses now.

I have some coding skills, so if there is an API ready for doing this I'd like to be pointed at. However I will not able to write something to ready to integrate in gnome, but I can give you something to start.