Okay, here's what I had to do to clear mine.
There is a file at /home/username/.gconf/apps/gnome-settings/gnome-panel/%gconf.xml that holds all the recently run commands. You can delete this by running:
rm -i /home/username/.gconf/apps/gnome-settings/gnome-panel/%gconf.xml
..but before you do that, take a look at the file to make sure it isn't used for anything else on your system. Mine only stores that stuff, but your's might not.
That isn't quite enough, though. Gnome also keeps the history in your current session data, and will recreate the file when you log out. Open up
in a text editor, and remove the line that starts with
ADD 3909091333 "def" "/apps/gnome-settings/gnome-panel" "IOR:01....
The number will probably be different for you, though. Just be sure to remove the whole line, even if your text editor wraps it. Then you can log out and back in again, and it will be cleared.
I would suggest that if you're doing something you want cleared that badly, you use a terminal and then run:
echo > /home/username/.bash_history
since that's easier. It's kind of cool to know how to both though.