1. A method of operating an internal combustion engine having at least one camshaft and a plurality of cylinders, each cylinder having at least one associated cam actuated intake valve, the method comprising:directing skip fire operation of the engine in accordance with a firing fraction that defines a first effective displacement of the engine, wherein during skip fire operation of the engine, for at least one of the cylinders, the cylinder is deactivated during selected skipped cylinder working cycles such that air is not pumped through the cylinder during the skipped cylinder working cycles and selected active cylinder working cycles are fueled and fired, the skipped and active working cycles being interspersed such that the one cylinder is fired, skipped and selectively either fired or skipped during successive work cycles in accordance with the firing fraction, while the engine is operating at the first effective displacement; and
controlling valve lift differently between the cam actuated intake valves associated with at least two of the cylinders such that the valve lift for the cam actuated intake valve associated with a first one of the cylinders is different than the valve lift for the cam actuated intake valve associated with a second one of the cylinders during a selected engine cycle, to thereby independently control an amount of air charge in the respective first and second cylinders during active working cycles that occur in the selected engine cycle; and
wherein at first selected time during operation of the engine, a first set of cylinders are operated in the skip fire manner concurrently with a second set of cylinders being operated using the variable lift control; and
at second selected times during operation of the engine, all of the cylinders in the first cylinder set are deactivated while the cylinders in the second cylinder set are operated using variable lift control.