I'm not sure what you mean by web application but with VMware Update Manager, you can upgrade ESX hosts and Linux/Windows guests systematically without any issues. I'm not sure what part of web applications are need to patch and VUM only applies to patches to the OS level only not on the application level so be aware to make sure its doable. If doable, then you can apply VUM to patches all the Windows 2008 servers you wish all at once but again its only OS level patches/upgrades and same to Host Update Utility but only apply to ESX host not guests though. Here is a guide for detail
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VMware vExpert 2009
iGeek Systems Inc.
VMware, Citrix, Microsoft Consultant
I'm familiar with that service. Problem is that the application is written & maintained in-house.
I was hoping there was a way I could build my updates into the Update Manager, so that I could distribute them without having to login to each server & install the updates.