Here are few notes on installing XenApp6 on Window Server 2008 R2 .
-1 used guide : http://www.danieletosatto.com/wp-content/uploads/2010/04/howto_install_configure_xenapp6_server_with_webinterface_license_server.pdf
0. I had troubles with IIS not able to start, installing IIS roles before XenApp6 solved the problem
1. follow the guide until “License Server Configuration” screen, I havn’t used XML Service IIS integration (as using this in my previous attempt coused IIS troubles mentioned in step 0.
2. generate trial license : http://carlwebster.com/blogs/webster/archive/2009/01/03/Learning-the-Basics-of-XenApp-5-for-Windows-Server-2008-Part-1-of-7.aspx
3. upload license to the XenApp 6 here : http://zenapp.blogspot.com/2010/04/installing-xenapp-6-part-3-citrix.html
4.configure XenApp6. (continue with the guide in #-1)
5. Publish application
6. in Citrix Web Interface Management create new XenAppService Site -> this will create PNAgent
7. Donwloaded client plug-in 12 for windows 64 bits
8. Manualy set up script folder http://support.citrix.com/article/CTX125107
9. Changed the pool for Script (CtxScriptPool) to enable to run 32bit applications http://forums.citrix.com/thread.jspa?messageID=1531112
10. Citrix plug-in client (finally) works
11. Changed the pool for Script (CtxAdminPool) to enable to run 32bit applications (WI now works too used the standard port 80)