A method of configuring a logic block of a programmable logic device (PLD) during physical implementation of a circuit design, wherein ports of the logic block are selectively registered, can include identifying the logic block of the PLD, wherein the logic block is located on a critical path. For each of a plurality of selectively registerable portions of the logic block, the method can include computing input slacks and output slacks based upon potential register usage within the logic block. The method further can include determining register usage for the logic block by maximizing a function which depends upon a measure of worst case slack for pipeline stages.