Great question and answer on
Server Fault:
$path = (Get-WmiObject -class "Win32_TSGeneralSetting" -Namespace root\cimv2\terminalservices -Filter "TerminalName='RDP-tcp'").__path
Set-WmiInstance -Path $path -argument @{SSLCertificateSHA1Hash="THUMBPRINT"}
Where THUMBPRINT is the thumbprint of the desired certificate.
