FileTraq was designed to be run periodically from the root crontab. Each time, it compares a list of system files with the copies that it keeps. Any changes are reported in diff or patchfile style, and dated backup copies are kept.
Yet Another File Integrity Checker saves information about the state of a filesystem to a database, which later can be used to compare against the current state of the filesystem, letting you know of any changed, added, or removed files.