There's a well known science fiction novel where a "programmer-archaeologist" on an interstellar fleet digs into a bunch of nested hypervisors and software nobody has touched in thousands of years, to find things still running on the unix time epoch.
The best part of that was, being a space-faring civilization, the narrator muses that its starting point is probably based on the date when humans first left Earth to go to the moon!
Jaron Lanier made an observation in one of his books about how technology concepts tend to get locked in, and predicted that MIDI has shaped digital music so much that in 1000 years we might still be stuck with its conceptual foundations.
(possibly You Are Not a Gadget, but could have been another)
I'd bet on tetris. I think there are more independent unlicensed implementations of tetris than any other game ever. Any particular implementation of it may wither away, but I bet if there are still programmers in a thousand years, there will probably be no shortage of tetris implementations.
I don't know - I have a 'prototype' application that, rather to my horror, I have found recently is still in production about 7 years after it should have been replaced by the 'real' system.
