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This is not actually something new but for anyone else that wants to quickly have a reference to it, here are two PowerShell scripts to stop and start BizTalk applications.

Stopping a specified Application:

if ($args.count -eq 0) {
  "You must specify the BizTalk Application name to stop!"
}
else{
    $BTSAppName = $args[0]
    $SQLInstance = "."
    $BizTalkManagementDb ="BizTalkmgmtdb"
    [void] [System.reflection.Assembly]::LoadWithPartialName("Microsoft.BizTalk.ExplorerOM")
    $Catalog = New-Object Microsoft.BizTalk.ExplorerOM.BtsCatalogExplorer
    $Catalog.ConnectionString = "SERVER=$SQLInstance;DATABASE=$BizTalkManagementDb;Integrated Security=SSPI"

    $BTSApp = $Catalog.Applications[$BTSAppName]
    if ($BTSApp.Status -ne "stopped")
    {
        "Stopping" + $BTSApp.Name
        $BTSApp.Stop("StopAll")
        $catalog.SaveChanges()
    }
    else
    {
        $BTSApp.Name + " is already stopped"
    }
}

Starting a specified Application:

</pre>
<pre>if ($args.count -eq 0) {
  "You must specify the BizTalk Application name to start!"
}
else{
    $BTSAppName = $args[0]
    $SQLInstance = "."
    $BizTalkManagementDb ="BizTalkmgmtdb"
    [void] [System.reflection.Assembly]::LoadWithPartialName("Microsoft.BizTalk.ExplorerOM")
    $Catalog = New-Object Microsoft.BizTalk.ExplorerOM.BtsCatalogExplorer
    $Catalog.ConnectionString = "SERVER=$SQLInstance;DATABASE=$BizTalkManagementDb;Integrated Security=SSPI"

    $BTSApp = $Catalog.Applications[$BTSAppName]
    if ($BTSApp.Status -ne "started")
    {
        "Starting " + $BTSApp.Name
        $BTSApp.Start("StartAll")
        $catalog.SaveChanges()
    }
    else
    {
        $BTSApp.Name + " is already started"
    }
}