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 http://www.vmware.com/pdf/vi3_vum_10_admin_guide.pdf

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Regards,

Stefan Nguyen
VMware vExpert 2009
iGeek Systems Inc.
VMware, Citrix, Microsoft Consultant

Windows and Linux updates are from http://shavlik.com - and I think that as long as they provide the update for your application you'll be able to do it. Otherwise - no

Unfortunately with the current version of VUM you won't be able to do this