You can do something along these lines (prototyping in PowerCLI)
$si=Get-ViewServiceInstance
$vmOpMgr=Get-View$si.Content.guestOperationsManager
$vmProcMgr=Get-View$vmOpMgr.fileManager
$spec=New-ObjectVMware.Vim.GuestProgramSpec
$spec.programPath="C:\myprogram.exe"
$spec.workingDirectory="C:\Temp"
$auth=New-ObjectVMware.Vim.NamePasswordAuthentication
$auth.interActiveSession=$false
$auth.username="domain\account"
$auth.password="mysecretpassword"
Get-View-ViewTypeVirtualMachine|%{ $vmProcMgr.StartProgramInGuest($_.MoRef,$auth,$spec) }
It will execute the program C:\myprogram.exe on all the VM and use the credentials passed through the $auth variable.