For those of you who want to work with BizTalk Server using PowerShell, check out the PowerShell BizTalk Provider on Codeplex at http://www.codeplex.com/PSBizTalk.
From the project page, the provider allows you to list all applications / orchestrations / schemas, stop an application, enlist an orchestration and use the full power of the shell to script away the pain of GUI based mass-management.