Check your framework of choice to see if the core files have been changed!

$ diff -rbB clean_source_code suspect_code_folder

the -rbB means "recursive and ignore whitespace differences" more-or-less.

This information was lifted from a very helpful Magento post at Inchoo, see the original at http://inchoo.net/magento/quickly-check-if-magento-core-files-are-modified/