WordPress File Monitor by Matt Walters monitors your WordPress installation for added/deleted/changed files. If a change is detected an email alert can be sent to your email inbox.
Monitors file system for added/deleted/changed files
Sends email when a change is detected
Multiple email formats for alerts
Administration area alert to notify you of changes in case email is not received
Ability to monitor files for changes based on file hash or timestamp
Ability to exclude directories from scan (for instance if you use a cacheing system that stores its files within the monitored zone)
Site URL included in notification email in case plugin is in use on multiple sites
Plugin homepage and install info, etc, at: http://mattwalters.net/projects/wordpress-file-monitor/.