cPanel updates will leave directories and files under your /home directory as well. Look for things like .cpupdates, .cpan, and the like. Essentially all that you should have under /home are your user folders and other things you may have created.
There is also the yum cache which is used when for system updates but once those updates are applied the cache files are no longer needed. You can clear this in SSH by doing 'yum clean all'.
The statistics software logs that Devon is speaking about will keep files in each user's tmp directory (ie /home/user/tmp/awstats). Cleaning these out will remove access statistics for the domain in question which I will usually leave the most recent month or two for them but how much history you leave for them is of course up to you.
Hope that helps!