Increase air pressure to 38-40psi (check the outside of your tire to make sure you don't go over the max), clean your intake filter, add fuel injector cleaner at every oil change or 3000 miles, go with 0w-30 oil, skinnier tires (running with the stock Civic size is better 185/65x14"), lighter wheels, wax your car, make sure your car is running in tip-top shape, make the underneath of your car flat (aka Lotus Elise), make sure you have 0 toe front and rear, and actually I would put your spare tire back in as it will level your car and make it more aerodynamic.

In my opinion without the spare the weight goes more onto the front of the car causing more drag.