RegSnap is a tool that can help you analyze changes made to the windows Registry. With it, you can compare saved snapshots and learn which keys were modified, deleted, or added.

You can also analyze other sensitive system parts, such as a list of files in Windows and Windows System directories, win.ini and system.ini files, and autoexec.bat and config.sys files.

RegSnap able to generate HTML reports, .REG files to undo and redo registry changes. Pro version supports command line interface and OLE Automation (i.e. could be scriptable from your programs).

Limitations:
30-day trial version is available for download. After 30 day trial period you must either stop using RegSnap or register it.