What finally made it start working

Two farm servers, a webinterface server doing double duty as the license server and a server for the data store.  All running Win 2008 R2.

Nothing was working.  The classroom instruction did not touch on the fact the Xenapp 6 out of the box would not function at all on a 2008 R2 box patched to SP1.  I found a lot of talk of hotfixes on the Citrix forums.  I installed the following 14 hotfixes (with a lovely reboot after each one) which actually started to make it work.

So, if you're about to embark on a vanilla Xenapp rollout to a bunch of 2008 R2 Sp1 systems, do not even try to use it until you've done each of these patches, and in this order.  There was a #12, but it was not necessary and was removed.

1_XA600W2K8R2X64010

2_XA600W2K8R2X64017

3_DSCXAGPMx100WX64001

4_XA600W2K8R2X64026

5_XA600W2K8R2X64029

6_XA600W2K8R2X64020

7_XA600W2K8R2X64021

8_XA600W2K8R2X64018

9_XA600W2K8R2X64012

10_XA600W2K8R2X64044

11_XA600W2K8R2X64056

13_XA600W2K8R2X64060

14_XA600W2K8R2X64058

15_XA600W2K8R2X64062

*edit #1:  Keep in mind that this information is only current as of the date of this posting.  If you're reading this in 2012, it's probably not quite as applicable.