Application of patches after core/module updates
If you find yourself doing this often then it might be beneficial to use a make file for the project. Then you can have your make file contain all the patches and just rebuild the codebase instead of updating in place.

Also, be sure to mark patches that you are using in production as "Reviewed and tested by community" this will make them more likely to be committed to the next release which will stop you from having to include that patch in the future.