A variety of methods and arrangements for controlling the operation of an internal combustion engine in a skip fire variable displacement mode are described. Generally, an engine is controlled to operate in a skip fire variable displacement mode. In the variable displacement mode, selected combustion events are skipped so that other working cycles can operate at better thermodynamic efficiency. More specifically, selected “skipped” working cycles are not fired while other “active” working cycles are fired. Typically, fuel is not delivered to the working chambers during skipped working cycles. In one aspect of the invention, a firing pattern is determined that is not fixed but the active working cycles are selected to favor the firing of working chambers that have recently been fired at least in part to reduce wall wetting losses. In another aspect of the invention, when an active working cycle follows a skipped working cycle in the same working chamber, the quanta of fuel injected for delivery to the working chamber is increased relative to the quanta of fuel that would be delivered to the working chamber when the active working cycle follows another active working cycle in the same working chamber in order to compensate for wall wetting losses that occur during skipped working cycles.