Are a trapezoid's diagonals ever perpendicular?

Yes, they can be. Here is an example to see how this is true. Construct two perpendicular lines AB and CD that intersect at a point O. Let AO = CO, BO = DO and AO ≠ BO, then ABDC forms an isosceles trapezoid. If the lines are not perpendicular, then also ABDC is an isosceles trapezoid and it has perpendicular diagonals.