Freedesktop.org (which provides some standards compatible with GNOME and KDE) suggests that shortcuts should appear in .desktop files. You can find out where an existing package places its .desktop files using the system package manager. For example, on Fedora:
$ rpm -ql transmission | grep desktop\$ /usr/share/applications/transmission.desktop
http://www.freedesktop.org/wiki/Howto_desktop_files is a tutorial that should help you get started.
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