For a networked control system, we consider the problem of encoder and controller design. We study a discrete-time linear plant with a finite horizon performance cost, comprising of a quadratic function of the states and controls, and an additive communication cost. We study separation in design of the encoder and controller, along with related closed-loop properties such as the dual effect and certainty equivalence. We consider three basic formats for encoder outputs: quantized samples, real-valued samples at event-triggered times, and real-valued samples over additive noise channels. If the controller and encoder are dynamic, then we show that the performance cost is minimized by a separated design: the controls are updated at each time instant as per a certainty equivalence law, and the encoder is chosen to minimize an aggregate quadratic distortion of the estimation error. This separation is shown to hold even though a dual effect is present in the closed-loop system. We also show that this separated design need not be optimal when the controller or encoder are to be chosen from within restricted classes.