5) The Snuke (season 11) The one spoofing 24 with a bomb inside Hillary Clinton
4) Mystery of the Urinal Deuce (Season 10) The one about the 9-11 conspiracy - conspiracy.
3) Trapped in the Closet (Season 9) The scientology episode.
2) Free Hat (Season 6) The one where the boys try to protect movies form their owners, and then the rednecks try to free Hat Mcllough. You have to see it.
1) Make Love, Not Warcraft (Season 10) Of course, the WOW episode. Epic.
Other great ones: With Apologies to Jesse Jackson (people who annoy you...), Smug Alert (Hybrids), ManBearPig (AL Gore...), Two Days Before the Day After Tomorrow (the global warming one, and the dam breaking), The Passion of the Jew (the Passion of the Christ one.)
Here's my top South Parks. Let's here yours.