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DiffView is a program written in C#.NET 3.5 SP1 and able to log modifications of a given program:

Make a diff into files (you can select folders to analyze in a treeview).
The program will give you a list of modified and created files within the specified range (in minutes)
Make a diff into registry (you can select keys to analyze in a treeview).
Quick scan (shows only modified keys within the specified range (in minutes))
Thorough scan (shows modified keys, and what has been modified - new / modified values, data). This scan needs to make a backup of targeted keys before to launch it
Generate a report of all modifications (files and registry)