My boss is looking for a comprehensive solution something like WinDiff, but a little different. Mainly he wants to be able to take the state of a machine (including registry and all files) on two different occasions and see the differences.

Are there any solutions out there? Preference to free, of course, but we're not opposed to commercial products.

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You could try "beyond compare" program or the compare plugin for Notepad ++

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Unfortunately those are only file system tools - we need registry as well – Wayne Werner Aug 4 '10 at 19:09
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Serverfault has a post asking the the same question.

TrackWinInstall looks like the best solution.

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