Advocacy of the primacy of skepticism is another of Dillahunty's recurring themes. He said at the American Atheists convention in Austin in 2013 that the closest thing he has to a motto is "to believe as many true things and as few false things as possible," taking his inspiration from David Hume. In the same lecture, he said that being a skeptic is the most important identifier of who he is. In addition, Dillahunty said that skepticism has something to say about untested religious claims, and that philosophical skepticism will lead to atheism. He sees atheism as a subset of skepticism, and he doesn't see why skepticism should not address religious claims, something that has become a point of controversy in the skeptic community. Dillahunty rhetorically asked, "how popular would psychics be, how popular would ghosts be, if there wasn't this monolithic idea that 70-80% of the population believe, that within each of us is an eternal soul that leaves the body when we're dead and either goes on to some afterlife or lingers around here on the earth?...If you teach people about what we know, about what most likely happens when we die, they will strive to treat people better while they're alive, and their grief will be lessened because they understand reality." He admonished "don't just do skepticism with the goal of getting it right, do it with the goal of not being able to get it wrong." In an interview published by the Norwegian Humanist Association, he said he doesn't see why religious claims about reality should be treated any differently by skeptics than conspiracy theories and allegations about alien visitation.
One of Dillahunty's recurring themes has been the superiority of secular morality over religious morality. His key contentions on the issue are that secular moral systems are inclusive, dynamic, encourage change, and serve the interests of the participants, whereas religious moral systems serve only the interests of an external authority. He touched on the subject again at a lecture at the 2013 American Atheists Convention in Austin: "They say we're immoral, when we're the only ones who understand that morality is derived from empathy, fairness, cooperation, and the physical facts about interacting in this universe. They've broken their moral compass and sacrificed their humanity on the altar of religion. They say we're lost and broken and in need of salvation, when we're the ones who are free." Dillahunty holds the view that advocating infinite reward or punishment for finite deeds is "morally inferior".
Dillahunty has spoken at atheist and freethought conferences around the world and has debated numerous Christian apologists, including Ray Comfort (on The Atheist Experience) and David Robertson on Premier Christian Radio's "Unbelievable."At the 2014 American Atheists Convention in Salt Lake City, he gave a workshop that outlined some key ideas in effective debating:
"Take the opponent seriously: The audience has to sense that I can perfectly understand their views, and have rejected them. Use logic: I tell them that I can write a better book than the Bible. Simple: I copy it word for word, except the parts about slavery. And don't forget emotion: It is theater. That is my advantage with a Baptist background over someone like Richard Dawkins, although he knows more about science."
He has also stated that he is willing to say "I don't know" in a debate, a "scary concept" to some of his audience.
Aside from people such as Ray Comfort and others who he has said he will not debate again, Dillahunty rejects the idea that debates are a waste of time:
"I am absolutely convinced from my experience and the evidence that I've gathered over the years of doing this that they are incredibly valuable."