Bair v. Shippensburg (2003)

In 2003, Jones heard the case of Shippensburg University students Walt Bair and Ellen Wray, who sued the school in an effort to stop enforcing a speech code. The speech code banned all "acts of intolerance" including racist, sexist, and homophobic speech. Jones ruled against the university, explaining that while the code had good intentions, it went too far in regulating speech. Jones issued an order that prohibited Shippensburg from enforcing four provisions of the Student Code of Conduct. Jones found that the government may not prohibit speech based solely on the impact it will have on the listener.

Kitzmiller v. Dover (2005)

Jones was assigned to the Kitzmiller v. Dover Area School District bench trial, the first direct challenge brought in federal court against a school district that mandated the teaching of intelligent design. He was praised by Tom Ridge, former Pennsylvania Governor and former head of the Department of Homeland Security, who said that "I can't imagine a better judge presiding over such an emotionally charged issue ... he has an inquisitive mind, a penetrating intellect and an incredible sense of humor."^[2]

On December 20, 2005, Jones ruled that the mandate was unconstitutional in a 139-page decision.^[3]

After the ruling was handed down, some pundits immediately attacked it, notably Bill O'Reilly on Fox News, who accused Jones of being a fascist and an activist judge. Casey Luskin and Jonathan Witt of the Discovery Institute, and activist Phyllis Schlafly, leveled similar charges.^[4] Jones also received death threats as a result of which he and his family were given around-the-clock federal protection.^[5]

In a speech to the Anti-Defamation League on February 10, 2006, he responded to critics who claimed that he had "stabbed the evangelicals who got him onto the federal bench right in the back"^[4] by noting that his duty was to the Constitution and not to special interest groups.^[6]

In a November 2006 talk given at Bennington College, Jones again rejected the "activist judge" criticisms and explained the role of the judiciary and how judges decide cases:

If you look at public polls in the United States, at any given time a significant percentage of Americans believe that it is acceptable to teach creationism in public high schools. And that gives rise to an assumption on the part of the public that judges should 'get with the program' and make decisions according to the popular will.

There's a problem with that. ... The framers of the Constitution, in their almost infinite wisdom, designed the legislative and executive branches under Articles I and II to be directly responsive to the public will. They designed the judiciary, under Article III, to be responsive not to the public will--in effect to be a bulwark against public will at any given time--but to be responsible to the Constitution and the laws of the United States.

That distinction, just like the role of precedent, tends to be lost in the analysis of judges' decisions, including my decision.^[7]

In 2008, Jones was awarded the American Humanist Association's Humanist Religious Liberty Award at the World Humanist Congress in Washington, D.C. In his acceptance speech, Jones explained how he was blasted by Bill O'Reilly, Phyllis Schlafly, and Ann Coulter for the decision in Kitzmiller v. Dover Area School District. Jones also remarked on the shortcomings of civics education and how the American public tends to have a limited understanding of the Constitution and the importance of the Establishment Clause of the First Amendment and separation of church and state established by the Founding Fathers of the United States. Jones gave his perspective on the separation of powers under the U.S. Constitution: "Articles 1 and 2 designate the legislative branch and the executive branch, respectively, as majoritarian—they are subject to the will of the people; they stand in popular elections. But article 3 is counter-majoritarian. The judicial branch protects against the tyranny of the majority. We are a bulwark against public opinion. And that was very much done with a purpose, and I think that it really has withstood the test of time. The judiciary is a check against the unconstitutional abuse and extension of power by the other branches of government." Jones added that Alexander Hamilton himself remarked: "Enthusiasm is certainly a very good thing but religious enthusiasm is, at least, a dangerous instrument."^[8]

Whitewood v. Wolf (2014)

In 2014, Jones presided over Deb Whitewood et al. v. Michael Wolf, a case in which the plaintiffs sought relief from Pennsylvania's Marriage Laws (23 Pa. C.S. § 1102). He delivered an opinion striking down the Pennsylvania statute barring same-sex marriage on May 20, 2014, on grounds that it unconstitutionally infringed the plaintiffs rights of due process and equal protection guaranteed by the Fourteenth Amendment to the U.S. Constitution. He did not attach a stay to his order, so the decision would be immediately effective.

In 2014, Jones appeared on CNN to discuss same-sex marriage and the law he anticipated would be applied by the U.S. Supreme Court.^[9]