I personally also make sure I have had the server backed up fully just in case!
I also stop the services prior to the upgrade and do a reboot of the server afterwards.
Qlik is one of the easiest pieces of software to upgrade in my opinion, I've never had one go wrong but its always better safe than sorry!
You might have already done the upgrade, but I'd also add to your check list the following:
1. Confirm you have the licence details for your server
2. A record of your reload tasks and schedules
3. A record of your CAL allocations.
4. Backup of your QlikView content (QVWs QVDs and any other content you're created)
As Adam mentions Qlik is nice to upgrade, but if things go wrong then you'll have the above information to restore the system on the same server or another if needed.
We backup the physical server that houses the QVS nightly. This includes C:\ProgramData\QlikTech, a C:\QVInclude folder we use and D:\ and E:\ drives that we use to house Software installs (D) and Source/User Docs (E). Qlikview V11 SR12 does not store configs in the registry correct? Meaning the backup of the file based configs should suffice. This will be my first time performing an in place upgrade of the application so trying to get all my ducks in line.