Unquestionably, South Park can be quite juvenile and overly scatological at times--but I also consider it to be one-of-if-not-the most biting and fearless satires on TV today! Just consider their infamous episodes skewering Scientology, anti-immigration panic, the pains of modern air travel, iTunes user agreements, the console wars, etc, etc, etc. I dare say that the series is actually improving with time, in sharp contrast to other animated comedies!
As you can plainly tell, my favourite South Park episodes are more sharp, biting satires and parodies than scatological and juvenile. As such, I generally prefer more recent episodes to the initial seasons (and so do Matt Stone and Trey Parker themselves).
My all-time favourite South Park episode thus far is Trapped in the Closet, which skewered Scientology by more-or-less simply presenting their core beliefs and indoctrination practices. (It's a true shame that it ultimately resulted in Scientologist Isaac Hayes leaving the show!)
Some of my other favourite episodes include Goobacks, Goth Kids 3: Dawn of the Posers, the Black Friday / A Song of Ass and Fire / Dragons and Titties trilogy, HUMANCENTiPAD, FunnyBot, Crack Baby Athletic Association, Free Willxyz, AWESOME-O, All About Mormons, A Ladder to Heaven, Super Best Friends, and How to Eat With Your Butt.
Trey Parker and Matt Stone, I salute you!