In my experience, an actual reprogramming of an ECU is only useful when changing other things away from stock, and sometimes that reprogramming is there to prevent check engine lights and to make what would be a non-street-legal change into one that can pass the smog requirements of the car. As others have said, depending on the car, the ECU can change the spark timing relative to the crank, the spark duration, the fuel injection timing relative to the crank, and the fuel injection duration. Some more modern engines can control the valve timing relative to the crank, or can control the throttle plate electronically, but that's really the limit of a chip. For real gains, you're going to need cams, exhaust flow, intake flow, compression, and timing changes.
Oh, and I wouldn't trust most "cold air intake" kits, especially when they stink air from under the hood instead of from outside like the factory intake systems do. That's more of a hot air intake than a cold one.