See also http://www.bvanleeuwen.nl/faq/?p=1236

Create vm list

$targets = Get-VM | Select Name, @{N="CBT";E={(Get-View $_).Config.ChangeTrackingEnabled}} | WHERE {$_.CBT -like "False"}

Enable CBT

ForEach ($target in $targets) {
   $vm = $target.Name
   $vmView = Get-vm $vm | get-view
   $vmConfigSpec = New-Object VMware.Vim.VirtualMachineConfigSpec
   $vmConfigSpec.changeTrackingEnabled = $true
   $vmView.reconfigVM($vmConfigSpec)
}

Create/Remove snapshot to enable CBT

ForEach ($target in $targets) {
   $vm = $target.Name
   Get-VM $vm | Get-Snapshot | Remove-Snapshot -confirm:$false
   New-Snapshot -VM (Get-VM $vm ) -Name "CBTSnap"
   Get-VM $vm | Get-Snapshot -Name "CBTSnap" | Remove-Snapshot -confirm:$false
}