I've asked this question before and received no answer: What South Park episode has a progressive message? And no, simply making fun of some idiotic conservative like Pat Robertson doesn't constitute a progressive message.
Dances with Smurfs comes to mind immediately. Best Friends Forever is another one (I believe congressional Republicans are literally depicted as tools of Statan). Passion of the Jew, the one about gay marriage where the Stan and Kyle have to keep that egg from breaking, the Imaginationland trilogy, World War Zimmerman, Cartman Sucks, Last of the Meehicans, and arguably (albeit to a lesser degree) Margaritaville, Cartoon Wars, Quest for Ratings, and Apologies to Jesse Jackson. There are probably others, but that seems like a good start even if you don't count the debatable ones.