Well I see a few potential uses. Some examples.
I see what do you mean but is there really such amount of tools which you run on regular base with different parameters each time? Samba, dhcp, ... these are configured only once (i.e. it doesn't matter if you write it into config file or into xml file), bzip & friends mostly have their GUI counter parts (ArcView comes into my mind) and well, 'ls' is more needed in bash than anywhere else (for GUI you have desktop explorer). Other use cases can be easily solved by "Set Application" desktop dialog where one can define default parameters etc..