Microsoft put out a new command-line tool called the File Checksum Integrity Verifier (FCIV) earlier this year. FCIV allows you to compute file hashes system-wide, and compare them to previous results using XML databases:
The File Checksum Integrity Verifier (FCIV) is a command-prompt utility that computes and verifies cryptographic hash values of files. FCIV can compute MD5 or SHA-1 cryptographic hash values. These values can be displayed on the screen or saved in an XML file database for later use and verification.
I am going to play around with this a bit, and see if it can be worked into FirstOnScene. Regardless, I will probably add this to my personal toolkit and use it for baselining systems as they head into production. This can easily turn into a poor man's HIDS with very little effort.