The application that I recommend for this operation is called Short Run. When executed it lists all currently available shortcuts even those of applications that have been uninstalled from the system. As you can see in the screenshot below entries pointing to uninstalled applications are represented with a exclamation mark.

A good way to start would be to remove all invalid shortcuts from the system. Just mark the shortcuts with the left mouse button and hold the CTRL key during that time to mark all at once. Pressing DEL will remove all selected entries from the system.

Far more interesting than removing invalid shortcuts is to add new shortcuts. Pressing CTRL A will open the menu where new shortcuts can be added. The Shortcut Name will be the name that you can enter in the run box after adding the shortcut. The file / folder form field contains the path to the file or folder that you want to open and the Optional Parameters field takes any optional program parameters.

Existing shortcuts can be edited as well. If you think that the shortcut name Thunderbird is to long you can edit it to “t”, “mail” or whatever else you like. The changes take effect immediately. Oh, and you can bring the Run Box to the front by pressing [Windows R].