Hacked!
The Hacked! module helps developers identify modified Drupal core, contributed modules, and themes by comparing installed files with their original versions. It highlights changes and can integrate with the Diff module and Drush for detailed analysis. This tool is intended for development environments only.
This module does not and will not prevent your site from being 'hacked'.
This module scans the currently installed Drupal, contributed modules and themes, re-downloads them and determines if they have been changed. Changes are marked clearly and if the diff module is installed then Hacked! will allow you to see the exact lines that have changed.
Hacked! also provides drush integration so that you can see what files have changed from the command line.
This is primarily a developer tool and should never ever (don't even think it) be installed on a production site.
Similar modules
There are a number of other 'integrity' modules, such as 'md5check', 'File integrity check' and 'Sentry'. These modules have features to protect a live site from code changes or to only check Drupal core.
Windows support
Windows is not currently supported by this module, if you want to write a patch to get it fully working, then please post it in the issue queue.