Ok so here is the first part with ALOT more to come after some fine tuning tomorrow…

Environment Run down:
XenApp 4.5, Web Interface 5.3, and NetScaler 9.2 this can be a VPX box.. Now for the fun stuff.

• First you will need to install IIS on a Win2k3 box yes this can be 64bit, that is what I have been using
  
• Change IIS port to match Current Farm’s XML Port, Restart IIS
  
• Now install XenApp 4.5, during the install select share XML port with IIS
  
• Now install Web Interface 5.3
  
• Create a site with the Access Gateway being the Authentication point (you will need at least a self-signed cert for this step for IIS)
  
• You will then want to select SmartCard, and SmartCard Pass-through (you will need to restart the server for this to take affect)
  
• Add the local machine as for the XML Service provider under the Site’s Farm Settings
  
• Add the local machine as the STA for Secure access
  

Now to the NetScaler

• Create an Authentication server using only Cert, then select Principal Name
  
• Create a virtual server
  
• Select the Server you create above as the authentication method
  
• Create a policy set it for ICA Proxy, then point to the Site you create above…
  

Things should now work

I will be posting a more detailed HOW-TO guide with a video for at least part if not all steps required.