I helped a friend update their Magento site from version 1.9.1 to 126.96.36.199. The software has a few ways to update, one using a command line utility and the other a web based service called Magento Connect. We used the latter to update and ran into a few issues before finally getting the site to update.
The first problem was the update process failed in Magento Connect with a message that there were conflicts between all the packages being updated. The root cause of this was inside the /public_html folder on the server was a folder called pkginfo which had a Latest_Mage_All.txt folder and another file. We needed to manually delete these and the updates ran as expected.
Once we got the updates to run, then the site returned a white screen. This was caused by an error in the Apache configuration on the server. Because Magento overwrites the .htaccess files, we needed to modify the file to suit the local configuration needs of the server. In this case, that meant SymLinksIfOwnerMatch. This resolved the issue and allowed the pages to load.
Once that was complete, we did need to delete the var/cache folder, as the site was having trouble showing a query that was no longer available in the latest version. That fix could have been prevented by turning off caching prior to updating, but was an easy enough fix nonetheless.
The final fix was template specific and cost us a new support fee with the good people at RocketTheme. The site for this nonprofit uses a module call RokMage HomePageGrid. The grid stopped working after the update, but the fix was simple. By adding the block to the allowed blocks permission page, the frontpage again populated with the necessary information.