The opening scenes and music refer to Buck Rogers in the 25th Century.. So do the robot dog, cat, and bird seen throughout the episode.
The Butterfly Effect is demonstrated here: when Kyle misses his ride in the present, everything on and around Cartman changes instantly 540 years in the future. Everything works uut when he gets to talk to Mrs. Garrison though - after Richard Dawkins walks out on Mrs. Garrison, everything is right in the future. :)
K-10 - K-9 (canine)
Kit-9 - Kitten
Cocka-3 - Cockatoo
All of these refer to Twiki, the robot from Buck Rogers in the 25th Century.
Some of the layout of the UAA bridge evokes the original USS Enterprise's bridge in Star Trek.
In last week's episode, the Allied Atheist Alliance was called the Allied Atheist Allegiance. The United Atheist League was called the Unified Atheist League. Ooops.
Crank Prank Time Phone is a truly retro phone - it has a cord attached to the base!
The Wise One is basically a Pope for the otters. When he tries to assert that wisdom is deeper and more reasonable than intelligence, he's killed for it. When Cartman fiddles with the past to get rid of Richard Dawkins, the Wise One is back with the others seeing Cartman off to the present.
Among the changes in Cartman's present is the Crank Prank Time Phone becoming the Crank and Wank Time Machine.
Some of the buildings in the UAA city look rather familiar - space shuttles with the front end buried into the ground (like the Caddies at Cadillac Ranch), tubes of lip stick, an inverted bowl...