Windows Run command list

Install Microsoft Tweak UI. Extract the zip file. Four files will be extracted. Right click on the file, "tweakui.inf," then click "install." Once installation is complete, go to the control panel. You should see a new icon, "Tweak UI." Once in the program, click on the "Paranoia" tab. Scroll down the window, check the box, "Clear Run History at Logon." Good Luck.

http://www.microsoft.com/ntworkstation/downloads/PowerToys/Networking/NTTweakUI.asp

The quickest way I can think of is to use Regedit and navigate to the following path

HKEY_CURRENT_USER\Software\Microsoft\Windows\CurrentVersion\Explorer\RunMRU

Delete ALL values (The items on the right hand pane)listed. They will be items like:

a notepad\1
b command\1
...

This is what TweakUI does as described in the other answer given. Most 'proper, quickest and efficient' is in the eyes of the beholder so I am not biased.

Hope this helps.