The plot in which the students have to vote between choosing douche and a turd as their new school mascot, and Stan's apathy to voting in that particular election is an allusion to the 2004 Presidential Election between George W. Bush and John Kerry. It satirizes the apathy of many voters who felt that both candidates were equally bad choices for President for different reasons.
Stan's exile from the town of South Park echoes that of Mazeppa, the eponymous hero of Lord Byron's poem, who is punished for having an affair with a countess by having his clothes torn off, then being tied to a horse which is driven out into the wilderness. Like Stan, Mazeppa is finally rescued.
The sub-plot of Stan being taken in by PETA from the wild but falling to disfavor by not following their marriage beliefs is a parallel of John Ferrier's story in "A Study in Scarlet", where Ferrier is saved from the wilderness by the Mormons and in return for being let into their society, promises to follow all of their beliefs but falls out of favor when he doesn't partake in their polygamist beliefs.
When P.Diddy does the Vote or die monologue the lady in the yellow is supposed to be J. Lo