How accurately have you measured your wheel circumference?

You are measuring different things. A cyclometer measures the rpm of the wheel as it passes by the sensor. since a rotation is a fixed distance, information can be calculated.

A gps measures point to point at timed intervals, so the gps records your position on the world, and assumes a straight line. Normally timing is 3 to 5 seconds and some gps systems allow you to change the time to increase battery life. GPX should be +/- 3 feet.

Even with gps, it depends on the frequency of data logging and the map topography used in the background.

I ride with Cyclemeter, a friend of mine rides with MapMyRide, over a 40 mile ride, he rides about 0.5 miles further.

I tend to like the gps system.