I’m blogging this so I don’t have to remember it (google searches never seem to turn up the right answer).
Start Biztalk: net start BTSSvc{YOURGUID-GOES-HERE-1234-567890ABCDEF}
Stop Biztalk: net stop BTSSvc{YOURGUID-GOES-HERE-1234-567890ABCDEF}
You can find out what GUID you need to use here by doing “tasklist /svc” from the command-line.