From Secrets of SharePoint – Tip of the Day

You can use Windows PowerShell to change a Web’s custom master page. Simply point the CustomMasterUrl to a new master page:

PS > $spWeb = Get-SPWeb http://SP01.powershell.nu

PS > $spWeb.CustomMasterUrl = “/_catalogs/masterpage/myNew.master”

PS > $spWeb.Update()

PS > $spWeb.Dispose()