Exhaust will definitely improve fuel mileage - that's all gains through efficency.
Intake shouldn't hurt or help much either way unless you drive it harder. Theoretically, it can net a mileage gain, but it would be small as efficient driving is characterized by the throttle being pretty closed.
Upgrading the ignition spark is a great idea, but is certainly out on the margins in gains, IMO.
Wide, soft tires will eat gas in a hurry, though.
Ovbiously, brake & suspension upgrades shouldn't have much impact on fuel mileage, but you will burn more trying to use them.
Basically, until you start playing with forced induction, cam timing, or fuel mapping, you shouldn't be able to hurt your efficency. (Except big tires and big wings.) Most basic bolt ons work by increasing efficency in the first place. It takes some radical ones to really dump more A/F into the engine when you don't need it.