I think the only episode that I've not liked was the one on conspiracy theories. And I agreed with them for the most part there, but what really bothered me was that they were arguing against conspiracy theories related to 9/11 by saying that they're disrespectful to the people who died in the attacks-- basically, trying to make conspiracy theorists stop theorizing through guilt.
I found that thinking repellent. Yes, I have very little time for the "truthers" and find their obsession just as annoying as anyone. But disagreeing about the reasons for a person's death is only disrespectful if you're blaming it on them. The truthers are generally saying that the government is actually behind the attacks to some degree or another. That might be wrong, even ridiculously wrong, but it's not disrespectful. Saying that it is just comes off to me as nationalism-- and even though P&T are staunchly anti-government, Penn at least does get nationalistic at times. He once did an entire radio show slamming other countries because some actress made an off-the-cuff comment about Americans being stupid. It was a dumb comment, but he really flew off the handle about it.
Penn would diverge sharply from Ron Paul on the subject of 9/11....Penn really does believe that "they attacked us for our freedoms." At least unlike conservatives he doesn't support doing away with those freedoms, but strangely (to me) he seems to be unable to avoid conflating the American people with the American government on that point.