Stan says, "Mr. Garrision, if we change our mascot, that means the eco-terrorists win!" This refers to all the warnings we got after 9/11 about changing our routines. We were to stay as normal as we were before, or the terrorists would notice, smell blood, and attack again. They would see our weakness and declare victory.
Giant Douche - voiced by Trey Parker, represents John Kerry. Turd Sandwich - voiced by Matt Stone, represents George W. Bush. The flag on the float Cartman was driving around in support of the Turd Sandwich is the same one used in the Bush-Cheney campaign signs.

More details added to the school: a short flight of stairs leading to the school offices and marble flooring (or was that linoleum?).
The Turd Sandwich calling the Giant Douche a turd sandwich is like Towelie calling Cartman a towel.
A hint of Jimmy appears in Stan's voice when he tells his mom he doesn't care about voting.
Did P Diddy go back to being called Puff Daddy?
The PETA Animal Sanctuary has some resemblance to Jurassic Park. Big Gay Al still takes in the gay animals.
Look at the background just before and when the PETA member stops to crap out in the open (15 minutes in) - you see Stevie Nicks there. :D

No, I did not flip the picture around. This is indeed a reversed PETA shirt the woman is wearing. Think she had time to dress that morning? :D
The ostrich-baby saying "Kill me" could be a reference to Alien Ressurection, where the group finds a twisted half-human, half-alien Ripley saying "Kill me." The mutant towel said this in Towelie as well.
Stan being banished and sent out into the wilderness echoes that of Mad Max being banished from a town because he would not conform to its way of life..