Microsoft File Checksum Integrity Verifier is a command line utility that computes and verifies hashes of files.
It computes a MD5 or SHA1 cryptographic hash of the content of the file. If the file is modified, the hash is different.
With FCIV, you can compute hashes of all your sensitive files. When you suspect that your system has been compromised, you can run a verification to determine which files have been modified. You can also schedule verifications regularily.