Important notes from the pre-reqs:

• Your Citrix License Server must be at Version 11.6.1 
• If you've still servers on Standard Edition they need to be migrated to Advanced
• All servers running the management console must be on Java SE Runtime Environment (JRE) 6 Update 14
• Once updated, run dscheck /full FTA /reindex on at least one server in the farm
• You must install Microsoft Visual C++ 2005 SP1 Redistributable Package on the servers

Specifically for x32 

• If you've got PSE450R04W2K3006 I think yo've got to uninstall it
  
• And PSE450R05W2K3039 is invalidated

Specifically for x64

• Make sure your 64-bit server is running Windows 2003 SP2
  
• And PSE450R05W2K3X64026 is invalidated

The rollup pack brings together a number of fixes - primarily around server administration - it does contain some security vunrability patches. 

You can read about the full list of fixes and download the rollup from the following links:

Hotfix Rollup Pack 6 for Citrix XenApp 5.0 and Citrix Presentation Server 4.5 for Microsoft Windows Server 2003 32-bit Edition

Hotfix Rollup Pack 6 for Citrix XenApp 5.0 and Citrix Presentation Server 4.5 for Microsoft Windows Server 2003 64-bit Edition

Have fun, don't forget to test it.