Found a very helpful write-up on how to get app-v installed on a Server 2k8r2 box.
They tech net articles are a little convoluted, while all the information is there, you have to find about 10 articles to get things set up.
Also, one of the things that I had issues with was the fact that .net 4 was installed on the servers. Make sure to uninstall .net 4 framework before trying to install app-v, unless you like scratching your head.
Remember to reinstall .net 4 after though
Cheers!