Wrote script so people specify the adfs server and the signature and encryption certificate will extract the certs to two files stored in c:\temp
# just put in the ADFS server name
$AdfsServer = 'adfs.microsoft.com'
[xml]$XmlDocument = (New-Object System.Net.WebClient).DownloadString("https://$AdfsServer/FederationMetadata/2007-06/FederationMetadata.xml")
#ADFS Signing Certificate
$Cert = $xmldocument.entitydescriptor.roledescriptor.keydescriptor | select Use,@{Name="x509"; Expression={(($_.keyinfo).X509data).x509certificate}}
#Sign Cert
$cert | ? {$_.use -eq "signing"} | select -ExpandProperty x509 | out-file c:\temp\Signcert.cer
#Encryption Cert
$cert | ? {$_.use -eq "encryption"} | select -ExpandProperty x509 | out-file c:\temp\Encryptioncert.cer
$Cert