Eyesite
Eyesite scans your directory structures, storing the details of every file in a database table. The details stored include the file date/time, size, and md5 checksum of the file. Every time Eyesite re-scans the directory structure, it re-calculates the md5 checksum of each file, and compares it to the one stored in the database. Eyesite is then able to detect any files in the directory tree that are new, changed, or deleted. If any changes are detected, Eyesite sends you an email.
With Eyesite, you can scan your site manually from the admin interface, or get the plugin to scan your site automatically at regular intervals. We sleep better at night knowing that Eyesite will tell us if anyone gets into any of our websites - and we'll know exactly which files were tampered with, so we can fix the problem fast.
The main status screen of Eyesite tels you which files have been added, changed, or deleted. The History screen shows the history of all past scans and administrative actions.