How to disable "There are unused items on your desktop"

Right-click on your desktop background and select [Properties].

From the "Display Properties" window, select the [Desktop] tab.

Select the [Customize Desktop...] button at the bottom.

Uncheck the "Run Desktop Cleanup Wizard every 60 days" box and click the [OK] button, and then click the [OK] button on the display properties window.

That should be it!

Run Command Most Recently Used List Storage

At least for Windows XP, this list is stored in the registry:

My ComputerHKEY_CURRENT_USERSoftwareMicrosoftWindowsCurrentVersionExplorerRunMRU

It looks like there are values a through z off of RunMRU, plus (Default) and MRUList. There is string value in MRUList: e.g., "nkvlsawbhczeyoijfugrtdxpmq", which determines the ordering of MRUList entries.