WWWBackup is designed to work this way. All source files and folders have to be in the same parent folder. This is Windows standard way of multiple selection. (e.g. in Windows Explorer, select multiple files and cut-&-paste)
It's not hard to create multiple backup tasks. If you need to create a lot of similar tasks on many computers, WWWBackup also has a command-line based interface, where you can invoke it from a batch file.
