Yeah it makes a difference.
You car is programmed to run on 87, you can run 89, 91, 92, 93, or 94, but the higher you go the less MPG you'll get and leave more carbon in the motor. Over time the carbon can foul the plugs and clog the cat.
Once you mod, and seroiusly mod, not just intake and exhaust, an increase in octane may be neccessary.
I have the reprogramed PCM in my car. It's programed to run on 91 or better. I go to Sunoco since they have the 91, I get 1 to 3 MPG better on 91 than on 93
