WILHELM SCREAM: in the episode, "Matriculated". It happens when the Sentinels attack the humans in the lab near the end.
There is a reference to the Visual Effects Supervisor for the Matrix films, John Gaeta, during "The Second Renaissance Part II." As the human army gathers in the trenches, preparing for Operation Dark Storm, a male voice on the P.A. system announces, "Lt. Gaeta, please report to the Ops Center. Lt. Gaeta to Ops Center."
At the end of Kid's Story, Kid's grave reads: "Michael Karl Popper, Beloved Son, Rest in Peace". (Karl Popper is a famous 20th Century philosopher)