If the files are not in the wastebasket and you don't have a backup then you will need to recreate them.
System queues can be recreated by copying the corresponding files from another machine. The file names for system files are ones with a low number. Otherwise, try using the "HKEY_LOCAL_MACHINE\SOFTWARE\Microsoft\MSMQ\Parameters\LogDataCreated" registry value.
Non-system queues will need to be recreated through Computer Management.