Not sure what else you've tried, but the example you have above is using an incorrect command name - the command is named "stop vm", not "stop". In all cases where the command name contains a space, you must put quotes around the entire command name.
This should work:
commandrun JFS3QESX008 "Surgient.Linux.ESX.stop vm" vm=1207fcaf-e9e3-7645-e69d-eb4cad1b63
The short name also works:
commandrun JFS3QESX008 "stop vm" vm=1207fcaf-e9e3-7645-e69d-eb4cad1b63
Hope this helps.