Monitor File Changes On Windows System

You are asking for a file integrity monitor (FIM), and I would suggest OSSEC. It runs natively on Windows and allows centralized configuration (if you need that).

Link: http://www.ossec.net

Another option is Verisys, a commercial, file integrity monitoring system for Windows.

I use Beyond Compare 2.

1. Right click on a directory, choose "Select Left Side to Compare".
2. Right click on another directory, choose "Compare to".
3. It lists all of the files in two vertical panes, showing the ones that are missing/changed/etc.
4. You can then drill down into each pair of files to see the changes at a file level.

It has quite a nice feature: if any files are different between a pair of directories, it changes the color of the icons. This allows you to instantly find any files that are different in the directory tree.