There are a number of ways to control the Folding@Home client. For me, one of the more useful things I can do by sending a command to the web client interface is to pause and resume the operation of the client. In particular, this is useful when running other CPU consuming tasks in automated scripts, etc.
So, from the prompt on the host running the Folding@Home client you can, for example, issue:
echo -e "pause 0\nquit" | nc localhost 36330
to pause the client. And then issue:
echo -e "unpause 0\nquit" | nc localhost 36330
to unpause (resume) the client. You can also access the control interface via telnet with this:
telnet localhost 36330
Type help <Enter> at the prompt for a list of commands and options.