I usually just make sure system status is all green, review some standard logs like distmgr, pkgxfermgr, etc. and then move on to the CU and any hotfixes. I suppose a lot depends on your change management process for ConfigMgr as well.
Jeff
Service Pack - CU (hours rather than days)
CU - Hotfixes (minutes rather than hours)
Also Monitor sitecomp.log and the Management Point Installation Logs (mpMSI.log, MPSetup.log). Also don't Close the Setup window until all steps are green! (Even when the Close Button is clickable..)
See Kent Agerlunds Blog Posts about the Management Point Installation issue, which might occur (In my case it did.): http://blog.coretech.dk/kea/upgrade-to-system-center-2012-r2-configuration-manager-sp
Great point about the setup window. . .definitely make sure all steps are green and successful.
Jeff