You can take a look at VMware VIX: http://www.engr.ucsb.edu/~duonglt/vmware/#vmware_vix which allows you to execute commands within the guestOS, so long as you have VMware Tools installed. The current version 1.6.2 supports up to ESX 3.5, but not vSphere, I've heard the next version will fully support vSphere in case you were looking to deploy VMs on ESX(i) 4.0
You could also use Windows run once reg. keys and if you have the scripts stored in some shared accessible repository such as an NFS server, you could easily copy them over and execute them. I also think if you deploy from a template, you have an option in the customization to run custom scripts as part of the deployment, I'm not 100% sure but I believe that is the case for Windows.
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William Lam
VMware vExpert 2009
VMware ESX/ESXi scripts and resources at:
VMware Code Central - Scripts/Sample code for Developers and Administrators
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