The Plugin Commander page is only visible from an individual blog, not from the Network Admin section. (Am I missing something? I looked everywhere for the Plugin Commander page in the Network Admin section.)
When I clicked "Deactivate all" on a plugin, Plugin Commander told me it had successfully deactivated it. I deleted the plugin file from the server. I then visited the plugins page for the same blog and got a message saying that that plugin had had to be deactivated because the file was missing. Apparently the "Deactivate all" link did not actually work.