I use blades. See attached. Depending on the number of users or what you do. I usually apply put a rule of 1 foreground/background methodserver per core. More cores per socket is better and faster. If you can put 4GIGs of ram is adequate per core butto 8GIGs per core is really good. Sometimes you need about 6GIGs to get you past a really big query or other large hitters like a Project Update.
For your Windows 2008 R2 Server CAD worker:
All installations to be placed on the NetApp/SAN/EVA/XPS/etc with all installs as aliases so you can just pull out the machine and pull it out and replace with a DNS alias change. Place all symbolic links and /usr into the SAN as well. That way you don't lose Java, Oracle links. Remember to save your profiles and OS parameter changes.
Externalize your vault and start considering using UnionFS, auFS or SquashFS so that you don't have to copy entire vaults or even entire Windchill installs. Your development server can just be server specific property filesand a separate installation of Cognos (or tailor your certificates to the server). You can place patches and service packs on a different layer without the need to make a complete backup. The intitial install will be placed on the NFS applicance. Just make sure you delete all the logs, and cache as a foundation base. Then the cache and logs will be server specific. This can also be applied to clusters where now you don't have to worry about class files being not sync'ed between servers. There is only one copy on the NFS appliance base and each slave is just property file layers which is server specific. This will save you tons of money in removing duplication of files accross systems which adds $$$ of storage requirements.
My system is running super fast with over 2000 publishes a day. Don't forget to put a test and development systems.
If you use a blade system, all your 16 possible blades can be connected together witha 10GIGE backbone switch which allows all servers to communicate at 10GIGe. You can then have your users connect to the core at 1GIGE.