I ran across this article on Host-based intrusion detection with samhain. There is an actively maintained FreeBSD port so I may try samhain. An alternative is AIDE, also with a FreeBSD port and an older 2001 article on using AIDE with Linux. The commercial standard is still Tripwire. Update: A cross-platform file integrity checker that works with Windows and UNIX is Another File Integrity Checker. You might also like md5deep.