Remove Alt-F2 history - Trying to remove password.
Solution 1:
To remove everything from the history just run
gsettings reset org.gnome.shell command-history
If you only want to remove some parts of the history, than it is easiest to just start dconf-editor and remove the unwanted command from the history under org->gnome->shell-> command-history.
Solution 2:
I don't use gnome ATM, but minor research came up with this for gnome3:
Install dconf-tools.
Run dconf Editor and navigate to /desktop/unity/runner/history
(from http://www.techques.com/question/24-122473/Delete-Alt-F2-history)