SimpleSiteAudit (SSA) is a PHP, script you upload onto your webhosting that continuously monitors the files on your webserver and contacts you if it detects any modifications, deletions or additions to the files on your server.
SSA will email you if it detects changes in any existing files, any new files appearing or any files are missing since it was last run.
Whilst SSA won't actually prevent you being hacked, you'll be notified as quickly as possible that your server may have been...