Alternate timeline similarities:
Carter still makes the "reproductive organs" line as she did in the pilot.
Jack left the Air Force and they want him back (whether his son accidentally shot himself with Jack's gun is not clear).
Samuels and two other Air Force officers still go to get Jack as they did in the pilot.
McKay still lusts after Carter.
The "USAF Advanced Research Institute" serves jello (and Carter still eats blue jello just like the SGC version).