There are many open source tools available to do this but I like the MD5summer program http://sourceforge.net/projects/md5summer/
It lets you create MD5 hashes of a folder or all the files in the drive. Once the program recursively hashes the files, it lets you save it as a file.
The program will list some of the “locked” system files that it couldn’t hash.
To test this program, I edited a text file and added “test” to the end, after that I ran the program to verify the hashes of current system snapshot with the saved snapshot.
Sure enough it generated a checksum mismatch for the edited files
It is a good idea to deselect the browser folders so that the history, cookies and bookmark files doesn’t trip the checksum mismatches
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