That's why I want to suggest the "module checksum" module. When you activate a module, the directory it is in is checksummed and the result stored. The module then allows you to rerun the checksum against all modules and shows for which modules the new checksum no longer matches. These are the modules that have been modified. With this list you can make sure you have the necessary patches before you upgrade said modules.
Best regards, Olivier
Just indicating that a module has been altered is too limited, IMO. Journal module (http://drupal.org/project/journal) recently implemented a "Patch log" feature (only available in latest dev snapshot currently), which allows you to keep track of any patches and hacks you applied to the modules on your site. This means you can lookup whether you can safely update to a later version of a module (given the possibility that your patch has been committed). Daniel