Have you ever come across a SharePoint installation that’s been customized in an unsupported way? You look at the 12 (or 14) hive and see that files have been modified by hand? Not good.
As you may know, changing core SharePoint files is unsupported and can lead to problems when patching.
The best way to clean up modified SharePoint installations is to pull out the customizations and move them into new files as part of a solution package (WSP file). That makes it easy to re-deploy customizations and ensures your environment will stay clean.