When clicking the File menu in WebMatrix 3 you will see a list of Recent Files and Recent Sites. I wanted to clear those entries and couldn't quite figure out how to do that. I searched the registry and explored the WebMatrix folder for some sort of configuration file.
In the folder
there is a Preferences sub-folder. I discovered that I can delete/rename that Preferences folder and the Recent Files and Recent Sites list will be cleared-out.
If anyone knows how to clear-out the Recent Files and Recent Sites lists without resorting to effectively deleting the Preferences folder, please advise. Otherwise, if you need to clear out those lists rest assured that WebMatrix will recreate the Preferences folder as well as its contents. However, you obviously might need to again specify some of the WebMatrix program settings that might have been lost.