Is there a cool way of performing CU updates for SQL Server on hundreds of machines?
The cool way is to use an unattended installation script that simply is called from each server, where the media for the installation is on a central directory on your network, that is accessible from each server. You will have to run the script in an elevated mode, which this is fairly easy in PowerShell.

You will need to use the CLI to extract the hotfix, I found that here. Then the CLI options for the SQL Server patch can be found here.

The following commands are what I used to apply the CU6 patch to the local SQL Server 2012 SP2 instance on my laptop. I changed to the directory I downloaded the hotfix to:

.\SQLServer2012-KB3052468-x64.exe /X:E:\Software\SQL_Server\2012\SP2_CU6\Extracted
cd Extracted
.\setup.exe /action=patch /instancename=SQL12 /quiet /IAcceptSQLServerLicenseTerms






You pretty much just work out writing this as a script for each server, then pull in that bit of the summary log (or just the whole log) to a central spot so you can go back and determine the status. Option 2 would be to just include a few lines of code to connect to each instance and verify the build number.