Doing remote system calls via SAMBA would be a bit tricky, I think you're correct in that SAMBA isn't really designed for that sort of thing.

You aren't the first to run across this issue though. There are a few other cross platform applications that do similar things to what you are attempting to accomplish. One in particular that I have in mind is called Big Brother. It can monitor various operating systems, including Linux and NT, from one central location. What they do is install a daemon (or service in the NT world) on each of the computers that need to be monitored. These daemons handle the the calls that can't be determined remotely.. ie, current disk usage, cpu usage, bandwidth utilization, etc.

They seem to have designed it well, in that it is reasonably simple to create a plug-in for it. If you don't want to spend the time creating this system yourself, you could always consider using Big Brother, and creating a plug-in for the functionality you wish to have. If it doesn't do what you want, you could always use it's system as an example.

They developed their own protocol (I believe) for the system to communicate with all the remote daemons it was monitoring. If you don't end up just creating a Big Brother plug-in, another method for creating such a beast would be to use SOAP or RPC, if you're boxes will have a web server running on them.

If you don't have a webserver, or you want to communicate via another network protocol, there is an excellent book on the subject called Network Programming with Perl by Lincoln Stein. Good luck!
-Eric