We just run a script which uses ESXUPDATE to apply the patches (in order of release) but does not reboot between them.
The whitepaper - http://www.vmware.com/pdf/esx3_esxupdate.pdf explains the options.
You may wish to centralise the patches, and perhaps deploy using HTTP or NFS if you have a large farm.
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I saw here scripted unattended patch install but myself preffered attended patch install but w/o rebooting. It works (was made here from others too) -significant is the sequence of the patches.