On small networks, I used plink (part of putty):
plink.exe -ssh 10.10.11.33 -l root -pw password /sbin/vmware-autostart.sh stop
This only stops automatically started VMs. To quote shutdown.sh:
#Power off autostart configured VMs
/sbin/vmware-autostart.sh stop
I am still trying to figure out how to use SSH keys with WinSCP and putty, as documented here.