I have multiple sites I manage that run WordPress so I try to stay up to date on all of them. If you stay on op of upgrading WordPress then most of the updates are fairly easy and don’t require changing that many files. Instead of uploading the entire set of files again it is easiest to simply upload the modified files. This will allow you to not have to make all of your custom modifications again if you have made customizations to any core WordPress files. Customizing core WordPress files is something I try to stay away from but there are definitely situations where I have modified core files to accomplish various goals. Anyhow since I haven’t found a site that keeps a consistant list of changed WordPress files I am going to try to start providing a list for each upgrade on Question Defense from now on.
When upgrading web applications it can make life much easier to get a list of files that have changed since the last version. This way you only have to overwrite a small number of files so if you won’t have to make all of your customizations again. The best application to use on Windows to do this is WinDiff. WinDiff is a very lightweight application that does not require installation to run. Below are some screenshots of WinDiff, where to download WinDiff, and instructions on how to compare two directories of like files.