Congress has the power to deny much if not most authority to the federal judiciary under the Exceptions Clause of the Article III. It has done so at least once before when it repealed part of the Habeas Corpus Act that was noted by the Supreme Court in Ex Parte McCardle. 74 U.S. 506 (1868)
During the Civil War Reconstruction, William McCardle, a newspaper publisher in Vicksburg, Mississippi, and not a member of the military, published some incendiary articles. He was jailed by the military commander, who was not amused, under a law passed by the United States Congress. McCardle invoked habeas corpus in the Circuit Court of the Southern District of Mississippi. The judge sent him back into custody, finding the military actions legal under Congress's law. McCardle appealed to the Supreme Court under a congressional act of 1867 that allowed federal judges to issue writs of habeas corpus and hear appeals from circuit courts. After the case was argued Congress repealed that particular act. The Court, speaking through Chief Justice Salmon P. Chase, validated congressional withdrawal of the Court's jursdiction. The basis for this repeal was the exceptions clause of Article III Section 2. You can read the entire decision at http://caselaw.lp.findlaw.com/scripts/getcase.pl?court=US&vol=74&invol=506
The court has no jurisdiction to hear cases on appeal except that granted by Congress. All the jurisidiction that the lower federal courts has is granted by Congress. In part of single session Congress could pass acts dealing with all the stupid issues facing the nation that the federal judiciary is always immersed in. The pledge of allegiance controversy come to mind.