CodeFN42 has released Kontakt LibOrganizer, a free utility for Windows that will let you easily change the order of all your libraries on the Libraries tab in Kontakt. With many libraries installed this can be quite time consuming to do this in Kontakt. In addition you can hide installed libraries you don't want to show.
Please note that this program only works with Kontakt 5. Windows only.
Warning: This program modifies entries in the Windows registry - use with caution.