Searching for disk alignments off the windows 2003 servers on VMware ESX i found a CLI script which can automate the search. The original site: http://ict-freak.nl/2009/12/15/powercli-check-partition-alignment-windows-vms-only/

Script:

$myCol = @()
$vms = get-vm | where {$_.PowerState -eq "PoweredOn" -and `
$_.Guest.OSFullName -match "Microsoft Windows*" } | Sort Name 

foreach($vm in $vms){
$wmi = get-wmiobject -class "Win32_DiskPartition" `
-namespace "root\CIMV2" -ComputerName $vm            

    foreach ($objItem in $wmi){
        $Details = "" | Select-Object VMName, Partition, Status
            if ($objItem.StartingOffset -eq "65536"){
                $Details.VMName = $objItem.SystemName
                   $Details.Partition = $objItem.Name
                $Details.Status = "Partition aligned"
            }
            else{
                $Details.VMName = $objItem.SystemName
                   $Details.Partition = $objItem.Name
                $Details.Status = "Partition NOT aligned"
            }
    $myCol += $Details
    }
}
$myCol | Export-Csv -NoTypeInformation "C:\PartitionAlignment.csv"
#$myCol | Export-Clixml "C:\PartitionAlignment.xml"