I highlighted my question below. Here is some background.
It's easy to find data showing the most commonly trojaned/modified Linux binaries and config files. ps, ls, find, kill, lsof, passwd, shadow, syslog.conf, etc. are all frequently changed after a system has been compromised. It's also easy to monitor utmp and wtmp to be alerted when a user logs onto a Linux system or when someone reboots the system.
Windows seems to be much more of a black box and more difficult in general to monitor. Part of this is due to the registry and lack of plain-text configuration files while part of it seems due to the closed-source, undocumented nature of Windows. And when I say, 'monitor' I mean know in real time that a file has changed through alerting (not logging). Send me an alert via sms, email, etc when X executable changes or when the local SAM file changes or when a virus reboots the system to install an infected MBR. And really, integrity monitoring is easy, the difficult part is knowing what files on Windows should be monitored. We can't monitor and alert on all files.
Is there an official list of commonly trojaned/modified Windows files that should be monitored by a HIDS?