I was reading Technote 4021466 which provides information on the Update Installer for Connections 2.0.1 when I noticed this The Update Installer for Lotus Connections provides the following functionality: Graphical user interface (GUI) support Silent installation option Installation and removal of individual and multiple-code updates Logging and tracking, recovery features and prerequisite handling So I am not sure how I missed this until now, but there is now a Graphical Installer for Lotus Connections Fixes and Fix Packs, this will make a lot of people very happy 
I am going to play with this a little more tomorrow, but this should make fixes and fix packs much simpler going forward. In addition there is also now a complete Lotus Connections 2.0.1 Fix List available
The graphical updater has been there since the original 2.0 fixes. The main problem with it was that it worked for fixes, but not fixpacks.
Hopefully they have this working by the time 2.0.1 FP1 comes out. Otherwise, we are back to digging for the secret fixpack ID.