The end of the Area 51 episode, when Penn refrains from insulting the UFO hunters because they're just a bunch of friends having a fun night, comes off as quite sweet—especially in comparison to the show's usual tone.
The end of the Boy Scout episode, where the scoutmaster admitted he was gay to all six of his "campers."
From the Eat This episode. Penn vouches for modified crops that can make greater yields and can grow in tougher places. Norman Borlaug, Noble laureate agricultural scientist whose "Green Revolution" have saved a BILLION people from starvation, explains:
Norman: You can't build a peaceful world on empty stomachs and human misery.
Penn's speech about his deceased parents during the episode about mediums who claim to speak with the dead, where he gives his reasoning as to why people like John Edwards are the biggest douches in the universe.
This was also Houdini's motive to begin debunking the mediums of the 1920s, after the loss of his mother and seeing his friend Arthur Conan Doyle, the creator of the ultra-rational character Sherlock Holmes, become involved with spiritualism over grief at the death of his son in World War One. Houdini told his wife to attempt contact by mediums prior to his death, with a code word to verify if it was him-none ever produced it.
At the end of the Life Coaching episode, Penn suggests that if you need help dealing with life's problems, instead of paying for a life coach, save that money and get something that will last... *leans on Teller* a friend.
From the "Stranger Danger" episode, Penn acknowledges that, even after her daughter was kidnapped, raped and murdered, Samantha Runnion's mother was still coming at it from a rational standpoint and they just couldn't make any wisecracks.
The segment in "Fast Food" where Penn takes time to interview the CEO of a major fast food chain (Andy Puzder of Carl's Jr.) and let him defend himself against people that like to blame fast food for America's obesity problems. Penn and Teller make a point of showing their audience that he's not, in fact, some soulless Corrupt Corporate Executive setting out to ruin people's health For the Evulz. He's just a normal guy trying to make an honest buck by selling food that people love—and he takes pride in his work, just like every honest man should.