A furnace controller for a modulating furnace that helps provide a balance between energy efficiency and occupant comfort across various burner firing rates and/or across various circulating blower speeds. In some cases, the furnace controller can be configured to permit a user to customize operation of the furnace in accordance with their particular needs and/or desires with respect to efficiency and comfort. A selection may be made between an energy efficiency setting and a user comfort setting. Then, a plenum parameter such as a discharge air temperature (DAT) or discharge air flow (DAF) may be regulated in accordance with the selected setting.