VaultPress knows which version of WordPress your site is running.
For each particular version of WordPress, we know what the MD5 checksum for each of the core files should be (an MD5 checksum is a kind of digital fingerprint for a file, that can be used to validate the integrity of that file).
As you can see here from this blog post, we’re using it on all of our properties and wouldn’t trust ourselves with anything else.
What are you using? Does your backup solution include this type of security measures?