How do I verify the integrity of my OSX installation? (Files, versions, and preferences) I want to verify the files, and configuration settings for my OSX installation against a known good reference "base".

Assuming I have two identical Macs (hardware), with one being factory installed and up-to-date in patches versus another as-is Mac.. how do I compare the differences between them?  Where do I look?

Although some people may use this answer as forensics, I'm looking more in the sense that I installed a few python libraries and am not sure what I did with them, and want to do some housekeeping.

Terminal commands (grep, ls, etc are all welcome).  Lacking an all encompassing solution, I'd appreciate your input on whatever you can contribute.
Mount both volumes on a Mac and drag both drives into a file comparison tool like Kaleidoscope. It will show file differences as well as hilight files that exist on one folder as opposed to the other folder.

You could also diff a file listing like ls -laR or whatever other flags you prefer to see what differences (excepting file metadata and ACL / special flags that either take other ls flags or are invisible to a simple file listing.) Some people go so far as to create a listing with md5 or other hashes that checksum the actual contents of files, but that's more appropriate for a security scan / configuration management suite like munki or tripwire.

Lots of blogs cover that sort of professional system management like these entries from 318, Inc.