In Gnome 3 it doesn't seem to be that easy yet. Here's a workaround though. Note that this should work for any application, but I can't try it with
rtorrent. Just report back if you have problems.
Let's find out the path of
rtorrent first. Open up a terminal and enter:
Remember this path. Then, try the following:
mkdir -p ~/.config/autostart
gedit rtorrent.desktop &
Gedit should open and let you edit this file. In this file, enter the following:
Where it says
/path/to/rtorrent, enter the path you've found out before. Then, save the file and close Gedit and the terminal. Now you need to restart Gnome and the application should start with your desktop session.