A programmable logic device has programmable phase-shifting circuitry. The phase-shifting circuitry is used to generate a set of skewed clock signals that is used to adjust the relative timing of device elements in a circuit synthesized in the programmable logic device. By suitably adjusting the relative timing of the device elements, the circuit critical path lengths are effectively reduced leading to improved circuit frequency performance. Algorithms are provided for establishing clock skew values that lead to improved circuit performance. The algorithms are incorporated in computer aided design tools to enable automatic optimization of circuit designs.