GA = General Availability
Newest version of BES is 4.1 SP5
The most important things to back up are:
1) Exchange mailbox stores (probably doing this already)
2) BESMgmt database (script I created to automate this
... then you can just back it up using a standard file agent)
In addition, I'd back up C:\Program Files\Research In Motion\BlackBerry Enterprise Server (and all its sub-folders) and also C:\Program Files\Common Files\Research In Motion (or wheverever you installed BES to).
Lastly, grab a system state backup; which'll include the registry.