We do the same thing in my organization. We rename the virtual machines, zz-[server name] and in the notes section put the date it was retired or moved to a different cluster if we cloned it for load balancing between cluster. Not only does this help to mark them but by putting zz- at the beginning it will move the server to the very bottom of your list of servers in your view so you dont see mixed off and on servers in your server list. 
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Re: vCenter VM rename problem
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