I'm not sure which Zones Of Thought book it was (probably Deepness in the Sky), but my favorite software joke in SciFi is when someone deep-diving into the system discovers that at the deepest layers timekeeping is still calculated from the UNIX epoch on the long lost human homeworld.

Reminds me of this: http://abstrusegoose.com/323

I wouldn‘t call it software archeology because it is still very much in use and modern standard.