Mayur,
What it means is that Cisco does not support the Windows Server configuration outside of what they detail in the Install Guide. What it also means is that if you have applications that need to be on that server (e.g., IBM BigFix, EMC Avamar, etc...) then go ahead and install them and/or configure the server the way you need it to, but if you have to contact TAC about an issue and they recognize something on the server that's not supported, they will ask you to remove or disable the software/service before they go any further with their support. This may not seem like a big deal, but if your call center is down and you're opening a P1 case, you don't want to waste any time.
With my experience, software doesn't seem to pose a problem... unlike these odd ball services that run in the background or crazy firewall rules or client side jobs that run in the middle of the day... it's things like that. Customers pushing back and using their own Windows Server image is not uncommon and you just hope that something doesn't go wrong after the cut over.
Since this is PCCE... just make sure nobody screws with Tomcat :)