The latest round for Patches from Magento (Supee-6788) have seemed to have caused a lot of confusion. While important, the patches fail to take into consideration that a few stock files may have been changed (.htaccess) or removed (.htaccess.sample). The patch also errors on cryptic messages and seemingly provide very little to troubleshoot with.
We have applied it to a few community edition Magento versions as well as an enterprise install and have had a mixed bag of results. We have documented a set of common tips that have helped us trouble shoot most of the issues with the new patch.