This script will look for GPOs which have no settings at all and delete them.

Import-Module GroupPolicy
$GPOs = Get-GPO -All
foreach ($GPO in $GPOs)
{
if (($GPO.Computer.DSVersion -eq 0) -and ($GPO.User.DSVersion -eq 0)) {
    write-host $GPO.DisplayName is an empty GPO.
    $GPO.DisplayName | Remove-GPO
    }
}