Microsoft provide a great tool to compare the difference between two systems, this program is Windows System State Analyzer.
First you create a snapshot of your system, then do some tasks (install program...) then create another snapshot at a later point of time so you can compare the two and see the changes.
I really like to use it in this situations:
1) you have to compare 2 cluster server that must have identical configuration
2) somebody install an application on your server and you want to know what happens behind the scene
3) you provide administrative rights to someone for a specific task and you want to be sure he didn't do anything else
More info here: http://blogs.technet.com/askperf/archive/2010/01/12/an-introduction-to-the-windows-system-state-analyzer.aspx
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